From be63b3d2cd0d3f9c4e82d6202a26b45f69d85165 Mon Sep 17 00:00:00 2001
From: Takuo Yasunaga <yasunaga@bio.kyutech.ac.jp>
Date: Sun, 7 Jun 2015 19:57:42 +0900
Subject: [PATCH] Modified: 	make Zephyr detach from base 	modified:  
 .gitignore 	modified:   Makefile 	modified:   src/Config/x86Mac64.inc 
 modified:   src/Objects/DataManip/dmFile/inc/dmFile.h 	modified:  
 src/Objects/DataManip/mrcImage/src/lmrcImageRadialDistribution.h 
 modified:   src/Objects/DataManip/pdbFile/src/pdbTrans.c New Class: eosBayes 
 new file:   src/Objects/General/eosBayes/

mrcImage3DPeakGet: under constrution
	new file:   src/Tools/mrcImage/mrcImage3DPeakGet/

mrcImageSNEstimate::
	new file:   src/Tools/mrcImage/mrcImageSNEstimate/src/usage.c
	new file:   src/Tools/mrcImage/mrcImageSNEstimate/src/util.c

mrcImageShapeSearch::
	modified:   src/Tools/mrcImage/mrcImageShapeSearch/src/mrcImageShapeSearch.c

pdb2mrc2d::
	modified:   src/Tools/pdbUtil/pdb2mrc2d/Config/OptionControlFile
---
 .gitignore                                         |   1 +
 Makefile                                           |  65 +++-
 src/Config/x86Mac64.inc                            |   2 +-
 src/Objects/DataManip/dmFile/inc/dmFile.h          |   2 +
 .../mrcImage/src/.lmrcImageShapePCA.c.swp          | Bin 0 -> 16384 bytes
 .../mrcImage/src/lmrcImageRadialDistribution.h     |   3 +
 src/Objects/DataManip/pdbFile/src/pdbTrans.c       |  23 +-
 src/Objects/General/Makefile                       |   0
 src/Objects/General/eosBayes/Config/Define.inc     |   3 +
 src/Objects/General/eosBayes/Config/Target.inc     |   0
 src/Objects/General/eosBayes/Makefile              | 132 +++++++
 src/Objects/General/eosBayes/doc/.eosBayes.html    |   0
 src/Objects/General/eosBayes/doc/.footer           |   0
 src/Objects/General/eosBayes/doc/.header           |   0
 src/Objects/General/eosBayes/doc/Makefile          |  41 ++
 src/Objects/General/eosBayes/inc/Makefile          |  31 ++
 src/Objects/General/eosBayes/inc/eosBayes.h        |  23 ++
 src/Objects/General/eosBayes/src/.CCHeader         |   0
 src/Objects/General/eosBayes/src/.CHeader          |   0
 src/Objects/General/eosBayes/src/.Ruby             |   0
 src/Objects/General/eosBayes/src/.Wish             |   0
 src/Objects/General/eosBayes/src/Makefile          | 345 +++++++++++++++++
 src/Objects/General/eosBayes/src/X86MAC64          |   1 +
 src/Objects/Makefile                               |   0
 src/Objects/Makefile.org                           |   5 +
 src/Tools/Config/Define.inc                        |   9 +
 src/Tools/mrcImage/.Source                         |   2 +
 src/Tools/mrcImage/.Source.org                     |   2 +
 .../mrcImage/mrcImage3DPeakGet/Config/Define.inc   |   4 +
 .../mrcImage3DPeakGet/Config/OptionControlFile     |   7 +
 .../mrcImage/mrcImage3DPeakGet/Config/Target.inc   |   0
 src/Tools/mrcImage/mrcImage3DPeakGet/Makefile      | 115 ++++++
 src/Tools/mrcImage/mrcImage3DPeakGet/doc/Makefile  |   2 +
 src/Tools/mrcImage/mrcImage3DPeakGet/inc/config.h  |   6 +
 .../mrcImage3DPeakGet/inc/mrcImage3DPeakGet.h      |  50 +++
 src/Tools/mrcImage/mrcImage3DPeakGet/src/.Depend   |   0
 src/Tools/mrcImage/mrcImage3DPeakGet/src/.Source   |   0
 src/Tools/mrcImage/mrcImage3DPeakGet/src/Makefile  | 427 +++++++++++++++++++++
 src/Tools/mrcImage/mrcImage3DPeakGet/src/X86MAC64  |   1 +
 .../mrcImage/mrcImage3DPeakGet/src/argCheck.c      | 107 ++++++
 src/Tools/mrcImage/mrcImage3DPeakGet/src/init.c    |  91 +++++
 .../mrcImage3DPeakGet/src/mrcImage3DPeakGet.c      |  69 ++++
 .../mrcImage3DPeakGet/src/mrcImage3DPeakGet.pane   |  17 +
 src/Tools/mrcImage/mrcImage3DPeakGet/src/usage.c   |  37 ++
 src/Tools/mrcImage/mrcImage3DPeakGet/src/util.c    |   4 +
 .../Config/OptionControlFile                       |   7 +-
 .../inc/mrcImageAutoCorrelationWithWindowing.h     |   4 +
 .../src/argCheck.c                                 |  11 +
 .../src/init.c                                     |   5 +
 .../src/mrcImageAutoCorrelationWithWindowing.pane  |  13 +-
 .../src/test/Makefile                              |  23 ++
 .../src/test/data                                  |   1 +
 .../src/usage.c                                    |   7 +-
 .../mrcImage/mrcImageSNEstimate/Config/Define.inc  |   4 +
 .../mrcImageSNEstimate/Config/OptionControlFile    |   6 +
 .../mrcImage/mrcImageSNEstimate/Config/Target.inc  |   0
 src/Tools/mrcImage/mrcImageSNEstimate/Makefile     | 115 ++++++
 src/Tools/mrcImage/mrcImageSNEstimate/doc/Makefile |   2 +
 src/Tools/mrcImage/mrcImageSNEstimate/inc/config.h |   6 +
 .../mrcImageSNEstimate/inc/mrcImageSNEstimate.h    |  46 +++
 src/Tools/mrcImage/mrcImageSNEstimate/src/.Depend  |   0
 src/Tools/mrcImage/mrcImageSNEstimate/src/.Source  |   0
 src/Tools/mrcImage/mrcImageSNEstimate/src/Makefile | 427 +++++++++++++++++++++
 src/Tools/mrcImage/mrcImageSNEstimate/src/X86MAC64 |   1 +
 .../mrcImage/mrcImageSNEstimate/src/argCheck.c     |  96 +++++
 src/Tools/mrcImage/mrcImageSNEstimate/src/init.c   |  91 +++++
 .../mrcImageSNEstimate/src/mrcImageSNEstimate.c    |  53 +++
 .../mrcImageSNEstimate/src/mrcImageSNEstimate.pane |  16 +
 src/Tools/mrcImage/mrcImageSNEstimate/src/usage.c  |  36 ++
 src/Tools/mrcImage/mrcImageSNEstimate/src/util.c   |   4 +
 .../mrcImageShapeSearch/src/mrcImageShapeSearch.c  |  25 +-
 .../pdbUtil/pdb2mrc2d/Config/OptionControlFile     |   1 +
 src/Tools/pdbUtil/pdb2mrc2d/inc/pdb2mrc2d.h        |   3 +
 src/Tools/pdbUtil/pdb2mrc2d/src/argCheck.c         |  11 +
 src/Tools/pdbUtil/pdb2mrc2d/src/init.c             |   4 +
 src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.c        |  18 +-
 src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.html     |  50 ++-
 src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.pane     |   3 +-
 src/Tools/pdbUtil/pdb2mrc2d/src/test/Makefile      |   5 +
 src/Tools/pdbUtil/pdb2mrc2d/src/usage.c            |   1 +
 80 files changed, 2685 insertions(+), 37 deletions(-)
 create mode 100644 src/Objects/DataManip/mrcImage/src/.lmrcImageShapePCA.c.swp
 mode change 100755 => 100644 src/Objects/General/Makefile
 create mode 100755 src/Objects/General/eosBayes/Config/Define.inc
 create mode 100755 src/Objects/General/eosBayes/Config/Target.inc
 create mode 100755 src/Objects/General/eosBayes/Makefile
 create mode 100755 src/Objects/General/eosBayes/doc/.eosBayes.html
 create mode 100755 src/Objects/General/eosBayes/doc/.footer
 create mode 100755 src/Objects/General/eosBayes/doc/.header
 create mode 100755 src/Objects/General/eosBayes/doc/Makefile
 create mode 100755 src/Objects/General/eosBayes/inc/Makefile
 create mode 100644 src/Objects/General/eosBayes/inc/eosBayes.h
 create mode 100755 src/Objects/General/eosBayes/src/.CCHeader
 create mode 100755 src/Objects/General/eosBayes/src/.CHeader
 create mode 100755 src/Objects/General/eosBayes/src/.Ruby
 create mode 100755 src/Objects/General/eosBayes/src/.Wish
 create mode 100755 src/Objects/General/eosBayes/src/Makefile
 create mode 120000 src/Objects/General/eosBayes/src/X86MAC64
 mode change 100755 => 100644 src/Objects/Makefile
 create mode 100755 src/Objects/Makefile.org
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/Config/Define.inc
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/Config/OptionControlFile
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/Config/Target.inc
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/Makefile
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/doc/Makefile
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/inc/config.h
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/inc/mrcImage3DPeakGet.h
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/.Depend
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/.Source
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/Makefile
 create mode 120000 src/Tools/mrcImage/mrcImage3DPeakGet/src/X86MAC64
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/argCheck.c
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/init.c
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.c
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.pane
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/usage.c
 create mode 100755 src/Tools/mrcImage/mrcImage3DPeakGet/src/util.c
 create mode 100755 src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/test/Makefile
 create mode 120000 src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/test/data
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/Config/Define.inc
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/Config/OptionControlFile
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/Config/Target.inc
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/Makefile
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/doc/Makefile
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/inc/config.h
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/inc/mrcImageSNEstimate.h
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/.Depend
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/.Source
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/Makefile
 create mode 120000 src/Tools/mrcImage/mrcImageSNEstimate/src/X86MAC64
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/argCheck.c
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/init.c
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.c
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.pane
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/usage.c
 create mode 100755 src/Tools/mrcImage/mrcImageSNEstimate/src/util.c

diff --git a/.gitignore b/.gitignore
index 89bfe803fe..57be6576b4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,6 +47,7 @@ optional/
 others/
 others2/
 tutorial/
+zephyr/
 
 #
 */*/*/*/*/*/*/tclIndex
diff --git a/Makefile b/Makefile
index 4d8ba6475b..39f992327e 100644
--- a/Makefile
+++ b/Makefile
@@ -9,8 +9,11 @@ EOS_GIT_REPOSITRY_DATA= git.sourceforge.jp:/gitroot/eos/data.git
 EOS_GIT_REPOSITRY_DATA_NOUSER=git://git.sourceforge.jp/gitroot/eos/data.git
 EOS_GIT_REPOSITRY_OTHERS= git.sourceforge.jp:/gitroot/eos/others.git 
 EOS_GIT_REPOSITRY_OTHERS_NOUSER=git://git.sourceforge.jp/gitroot/eos/others.git
+EOS_GIT_REPOSITRY_ZEPHYR= git.sourceforge.jp:/gitroot/eos/zephyr.git 
+EOS_GIT_REPOSITRY_ZEPHYR_NOUSER=git://git.sourceforge.jp/gitroot/eos/zephyr.git
 
 EOS_GIT_REPOSITRY_HOSTDEPEND=git.sourceforge.jp:/gitroot/eos/hostdepend
+EOS_GIT_REPOSITRY_HOSTDEPEND_NOUSER=git://git.sourceforge.jp/gitroot/eos/hostdepend
 
 help::
 	@echo ">> Help"
@@ -26,11 +29,12 @@ help::
 	@echo " $$ make git-merge       or git-merge[-all|-data|-tutorial|-optional|-others]" 
 	@echo " $$ make setting"
 	@echo "---- To init git repository ----"
-	@echo " $$ make git-init        or git-init[-all|-data|-tutorial|-optional|-others]" 
+	@echo " $$ make git-init        or git-init[-all|-zephyr|-data|-tutorial|-optional|-others]" 
 	@echo "---- To clonse git repository ----"
-	@echo " $$ make git-clone or git-clone[-all|-data|-tutorial|-optional|-others]" 
+	@echo " $$ make git-clone or git-clone[-all|-zephyr|-data|-tutorial|-optional|-others]" 
 	@echo "---- option ----"
 	@echo "     [] : base only"
+	@echo "     [-zephyr]   : zephyr (for GUI/browser)"
 	@echo "     [-data]     : data (for test)"
 	@echo "     [-tutorial] : tutorial"
 	@echo "     [-optional] : optional(for documents)"
@@ -257,7 +261,10 @@ git-push-with-check::
 		fi; \
 	fi;
 
-git-fetch-all:: git-fetch git-fetch-data git-fetch-optional git-fetch-tutorial git-fetch-others
+#
+# fetch
+#
+git-fetch-all:: git-fetch fit-fetch-zephyr git-fetch-data git-fetch-optional git-fetch-tutorial git-fetch-others
 
 git-fetch::git-pull-hostdepend
 	@echo "fetch: base directory" 
@@ -268,6 +275,9 @@ git-pull-hostdepend::
 	@echo "pull: hostdepend directory"
 	@cd hostdepend/$${EOS_HOSTDIR}/; git pull hostdepend$${EOS_HOSTDIR} master || echo "No files to be fetched" 
 
+git-fetch-zephyr::
+	cd zephyr; git fetch zephyr master --tags		; git log -1
+
 git-fetch-data::
 	cd data    ; git fetch data master --tags		; git log -1
 
@@ -280,11 +290,17 @@ git-fetch-tutorial::
 git-fetch-others::
 	cd others  ; git fetch others master --tags		; git log -1
 
-git-merge-all:: git-merge git-merge-data git-merge-optional git-merge-tutorial git-merge-others
+#
+# merge
+#
+git-merge-all:: git-merge git-merge-zephyr git-merge-data git-merge-optional git-merge-tutorial git-merge-others
 
 git-merge::
 	cd .       ; git log -1; git merge FETCH_HEAD 
 
+git-merge-zephyr::
+	cd zephyr  ; git log -1; git merge FETCH_HEAD 
+
 git-merge-data::
 	cd data    ; git log -1; git merge FETCH_HEAD 
 
@@ -301,7 +317,8 @@ git-merge-others::
 # Nickname 
 #
 
-git-init-all:: git-init git-init-data git-init-optional git-init-tutorial git-init-others
+# init
+git-init-all:: git-init git-init-zephyr git-init-data git-init-optional git-init-tutorial git-init-others
 
 git-init:: git-add-hostdepend
 	if [ ! -d .git ] ; then git init	; fi
@@ -315,6 +332,13 @@ git-init-data::
 	@export ORIGINNAME=data; \
 	make git-remote-add-data;
 
+git-init-zephyr::
+	if [ ! -d zephyr ] ; then mkdir zephyr ; fi
+	cd zephyr; \
+	if [ ! -d .git ] ; then git init	; fi ;
+	@export ORIGINNAME=zephyr; \
+	make git-remote-add-zephyr;
+
 git-init-optional::
 	if [ ! -d optional ] ; then mkdir optional; fi
 	if [ ! -L doc      ] ; then ln -sf optional/doc . ; fi
@@ -342,6 +366,8 @@ git-init-others2::
 	if [ ! -d others2 ] ; then mkdir others2; fi
 	cd others2 ; git remote add others2 $${EOS_GITUSER}@$(EOS_GIT_REPOSITRY_OTHERS)
 
+# clone
+
 git-clone-all:: git-clone
 	@if [ ! -z "$${EOS_HOME}" -a -d "$${EOS_HOME}" ] ; then \
 		cd $${EOS_HOME} ; \
@@ -365,6 +391,20 @@ git-clone::
 		fi; \
 	fi;
 
+git-clone-zephyr::
+	if [ ! -d zephyr] ; then mkdir zephyr; fi
+	@cd zephyr;  if [ ! -d .git ] ; \
+	then \
+		if [ -z $${EOS_GITUSER} ] ; then \
+			git clone --depth 1 $(EOS_GIT_REPOSITRY_ZEPHYR_NOUSER) ./ ; \
+		else \
+			git clone --depth 1 $${EOS_GITUSER}@$(EOS_GIT_REPOSITRY_ZEPHYR) ./; \
+		fi ; \
+		cd ../ ; \
+		export ORIGINNAME=zephyr; \
+		make git-remote-add-zephyr; \
+	fi
+
 git-clone-data::
 	if [ ! -d data ] ; then mkdir data; fi
 	@cd data;  if [ ! -d .git ] ; \
@@ -422,7 +462,9 @@ git-clone-others::
 		export ORIGINNAME=others; \
 		make git-remote-add-others; \
 	fi
-
+#
+# add
+#
 git-remote-add::
 	@if [ ! -z "$$ORIGINNAME" -a ! -z "$${EOS_HOME}" -a -d "$${EOS_HOME}"  ]; then \
 		cd $${EOS_HOME}; \
@@ -434,6 +476,17 @@ git-remote-add::
 		fi ; \
 	fi;
 
+git-remote-add-zephyr::
+	@if [ ! -z "$$ORIGINNAME" ]; then \
+		cd $$ORIGINNAME; \
+		SSS=`git remote -v | awk '{print $$1}' | grep data`; if [ ! -z "$$SSS" ] ; then git remote rm zephyr; fi ; \
+		if [ -z $${EOS_GITUSER} ] ; then \
+			git remote add zephyr $(EOS_GIT_REPOSITRY_ZEPHYR_NOUSER); \
+		else \
+			git remote add zephyr $${EOS_GITUSER}@$(EOS_GIT_REPOSITRY_ZEPHYR); \
+		fi ; \
+	fi;
+
 git-remote-add-data::
 	@if [ ! -z "$$ORIGINNAME" ]; then \
 		cd $$ORIGINNAME; \
diff --git a/src/Config/x86Mac64.inc b/src/Config/x86Mac64.inc
index d6bc494977..a9dbf95401 100755
--- a/src/Config/x86Mac64.inc
+++ b/src/Config/x86Mac64.inc
@@ -278,7 +278,7 @@ INCCUDA = -I$(EOS_HOME)/util/$(OSTYPE)/cuda/inc -I$(EOS_HOME)/util/$(OSTYPE)/cud
 #LIBCUDA = -L$(EOS_HOME)/util/$(OSTYPE)/cuda/lib64 -L$(EOS_HOME)/util/$(OSTYPE)/cuda/lib64 -lcudart -lcufft
 LIBCUDA = -L$(EOS_HOME)/util/$(OSTYPE)/cuda/lib -lcudart -lcufft
 
-#HOSTDEPENDENTLIB += $(LIBCUDA)
+HOSTDEPENDENTLIB += $(LIBCUDA)
 
 
 
diff --git a/src/Objects/DataManip/dmFile/inc/dmFile.h b/src/Objects/DataManip/dmFile/inc/dmFile.h
index c68ef96c4f..e17a707317 100644
--- a/src/Objects/DataManip/dmFile/inc/dmFile.h
+++ b/src/Objects/DataManip/dmFile/inc/dmFile.h
@@ -135,6 +135,7 @@ typedef struct dmFile3Tag {
 	char           seperator[4];
 	dmFileInteger4 ninfo; 
 	dmFileInteger4* info; 
+	long            pValue; // Offset	
 	void*           value;  // Array or value 
 	void**          value2; // Struct
 	void**          value3; // Array of Struct
@@ -151,6 +152,7 @@ typedef struct dmFile4Tag {
 	char           seperator[4];
 	dmFileInteger8 ninfo; 
 	dmFileInteger8* info; 
+	long            pValue;
 	void*           value;  // Array or value 
 	void**          value2; // Struct
 	void**          value3; // Array of Struct
diff --git a/src/Objects/DataManip/mrcImage/src/.lmrcImageShapePCA.c.swp b/src/Objects/DataManip/mrcImage/src/.lmrcImageShapePCA.c.swp
new file mode 100644
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zt2d&STd9Y5R67i;Upud~ChdidXy=sz+5-cw(HU@wAYgRQeRE^eGviYSlw`bOHVqq3
zRz8+wsS!}(G<+OABIyJrt{KsM5IuscKBVM~!_Kg1_|b9-ozbrpDy(Wt6hS~bcHHs<
z+v`j?@81(8;&}c$Lc+*od?!R<_pvM9PF@&Ux*TApyNbAuR7KEHwY`z5h$yPIR;Y^S
zw0J(T6HGs>m3KNBk7uiJNE`$C;8iguc%4pe2tjegm%!6ni|O8zFsX50&=T-~?#az$
zsgRjr)2fBRLR{}PPfjt_VhuasJoli*UjbS>HDh4+UZz%=HI-|jz<nJMmbqY?3${ao
zZ4^WWm$~3_NN^biVL=0V78#Meyv9(yYFc-)IvwVY2$v5*B9h`cKf{F_cO=yKbnvPj
zx>^o&jA8yxg6`$#u2<q0@SzwX()<$dQNTmx7m5$O5is>YyUu2qs*AYxd@v+MjWj%8
z-}9hPGb(zs%4j^7k32_m3vo<5ZG5L*p_K*IqDPN5DwW1jt$LWhDa8{HCn9z5V73zD
zi6M%lWP^#(1cg+5h@|tR4`<FF9ky*|@UP$9%ee+#d+1<v;G%&#BNl_kDxGh;r9Gr!
zn!+~eBYpJ10)N8V$Zy)LgI}&cF_xgJO%rnvp@~Vj_7H#y`8474|K~CPy%_UiKK~c{
z`%hy&zX|vgbM+sASAjv`E6mML0$YGnn3KN@JO!kHk1_Xt6!-<Y_?-JjU>mR%xDL1!
z;C40x@+TRP3`hnf1CjyBfMh^2@b57YUK?@OKEtazeCd6pjTr{!MeaTTR+UpJ{%+~-
z1oU2g$1-guv;h!V_V2maAGH=X)@$2=n+h)0^6iIE0rnhvEnr7m$9Flx_SV=qfA8Zw
zw!-a-+F4t>RyBh)`H^tMQoUlOyL&cDIq#hn%3{607%1ySTBso*-A)tMquF26-`-h!
zkLKT~);R9wULm(5)w4N)JS&t3xL7#;*nNr?Vz;AbR)p<ETX;c@@f7q8^0Zh(13Mgd
zHFNbAaRaNhXuaBza-)75!s@-=<Ead$Ry5tvYg1Sn?%KTRkP~%#JzD)#E3S}g!M(jg
lu2fn>Fwi4;-j{l8czWesBhi3c+^ek-^U*eklJD=>{tHl13h@8{

literal 0
HcmV?d00001

diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageRadialDistribution.h b/src/Objects/DataManip/mrcImage/src/lmrcImageRadialDistribution.h
index 488a225223..e064b5be41 100755
--- a/src/Objects/DataManip/mrcImage/src/lmrcImageRadialDistribution.h
+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageRadialDistribution.h
@@ -20,6 +20,9 @@ typedef struct lmrcImageRadialDistributionInfo {
 	float Cx;
 	float Cy;
 	int flagAverage;
+	int flagAzimuth;
+	int NAzimuth;
+	floatVector* azimuth;
 } lmrcImageRadialDistributionInfo;
 /* struct end */
 
diff --git a/src/Objects/DataManip/pdbFile/src/pdbTrans.c b/src/Objects/DataManip/pdbFile/src/pdbTrans.c
index d3a33ea9f4..e05047bb6d 100755
--- a/src/Objects/DataManip/pdbFile/src/pdbTrans.c
+++ b/src/Objects/DataManip/pdbFile/src/pdbTrans.c
@@ -17,6 +17,7 @@ static char __sccs_id[] = "@(#)pdbTrans ver1.1; Date:96/07/13 @(#)";
 #include <time.h>
 
 #define DEBUG
+#undef DEBUG2
 #include "../inc/pdbFile.h"
 #include "String.h"
 #include "eosCuda.h"
@@ -103,6 +104,18 @@ pdbTrans(pdbFile* pdb, Matrix3D Matrix)
 	} else {
 		floatVectorInit(&v, 4);
 		v.data[3] = 1.0;
+
+#ifdef DEBUG
+	{
+		int ii, jj;
+		for(ii=0; ii<4; ii++) {
+		for(jj=0; jj<4; jj++) {
+			DEBUGPRINT1("%f ", Matrix[ii][jj]);
+		}
+			DEBUGPRINT("\n");
+		}
+	}
+#endif
 		pdbFileTop(pdb);
 		while(1) {
 		  if(0==strncmp(pdb->PDB->Record, pdbRecordAtom,       PDB_FILE_RECORD_LENGTH)
@@ -114,10 +127,12 @@ pdbTrans(pdbFile* pdb, Matrix3D Matrix)
 
 			matrix3DMultiplyVector(&v, Matrix);
 
-			//DEBUGPRINT3("%f %f %f\n", Matrix[3][0], Matrix[3][1], Matrix[3][2]);
-			//DEBUGPRINT2("x %f -> %f\n", pdb->PDB->Coord.x, v.data[0]);
-			//DEBUGPRINT2("y %f -> %f\n", pdb->PDB->Coord.y, v.data[1]);
-			//DEBUGPRINT2("z %f -> %f\n", pdb->PDB->Coord.z, v.data[2]);
+#ifdef DEBUG2
+			DEBUGPRINT3("%f %f %f\n", Matrix[3][0], Matrix[3][1], Matrix[3][2]);
+			DEBUGPRINT2("x %f -> %f\n", pdb->PDB->Coord.x, v.data[0]);
+			DEBUGPRINT2("y %f -> %f\n", pdb->PDB->Coord.y, v.data[1]);
+			DEBUGPRINT2("z %f -> %f\n", pdb->PDB->Coord.z, v.data[2]);
+#endif
 
 		    pdb->PDB->Coord.x = v.data[0];
 		    pdb->PDB->Coord.y = v.data[1];
diff --git a/src/Objects/General/Makefile b/src/Objects/General/Makefile
old mode 100755
new mode 100644
diff --git a/src/Objects/General/eosBayes/Config/Define.inc b/src/Objects/General/eosBayes/Config/Define.inc
new file mode 100755
index 0000000000..025e2b0d7a
--- /dev/null
+++ b/src/Objects/General/eosBayes/Config/Define.inc
@@ -0,0 +1,3 @@
+OBJECTNAME = eosBayes
+EXTRA_INC =
+EXTRA_CCOPTS =
diff --git a/src/Objects/General/eosBayes/Config/Target.inc b/src/Objects/General/eosBayes/Config/Target.inc
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Objects/General/eosBayes/Makefile b/src/Objects/General/eosBayes/Makefile
new file mode 100755
index 0000000000..75b467d674
--- /dev/null
+++ b/src/Objects/General/eosBayes/Makefile
@@ -0,0 +1,132 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+DIRS = src inc doc
+
+all:
+	for dir in ${DIRS} ; \
+	do \
+		$(CD) $${dir}; $(MAKE) all; $(CD) ..; \
+	done
+
+install:
+	for dir in ${DIRS}; \
+	do \
+		${CD} $${dir} ; $(MAKE) install; $(CD) ..; \
+	done
+
+debug:
+	for dir in ${DIRS} ; \
+	do \
+		$(CD) $${dir}; $(MAKE) debug; $(CD) ..; \
+	done
+
+install-debug:
+	for dir in ${DIRS}; \
+	do \
+		${CD} $${dir} ; $(MAKE) install-debug; $(CD) ..; \
+	done
+
+clean:
+	for dir in ${DIRS} ; \
+	do \
+		$(CD) $${dir}; $(MAKE) clean; $(CD) ..; \
+	done
+
+depend:
+	for dir in ${DIRS} ; \
+	do \
+		$(CD) $${dir}; $(MAKE) depend; $(CD) ..; \
+	done
+
+put:
+	for dir in ${DIRS} ; \
+	do \
+		$(CD) $${dir}; $(MAKE) put; $(CD) ..; \
+	done
+
+check:
+	@cd src; \
+	if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+                echo making directory; \
+                mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+        fi 
+	ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+	@$(RM) -f src/Makefile
+	@$(RM) -f inc/Makefile
+	@$(RM) -f doc/Makefile
+	@$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+	@$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/inc/Makefile inc/Makefile
+	@$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/doc/Makefile doc/Makefile
+	@rm -f src/.Depend src/.Source
+	@touch src/$(OSTYPE)/.Depend
+	@touch src/$(OSTYPE)/.Source
+	@touch src/.CCHeader
+	@touch src/.CHeader
+	@touch src/.Wish
+	@touch src/.Ruby
+	@cd inc; make install
+	@cd src; make install-ascii
+
+#
+# CVS
+#
+cvsupdate:: 
+	cvs -d $(EOS_CVSROOT) update -d   
+
+cvscommit::
+	cvs -d $(EOS_CVSROOT) commit -R
+
+#
+# Backup
+#
+backup:
+	@cd ../../../.. ; \
+	echo $(OBJECTNAME) ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]*;  \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.*; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*
+
+backup-all:
+	@cd ../../../.. ; \
+	echo $(OBJECTNAME) ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]*;  \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.*; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*
+
+#
+# Distribution
+#
+distribute:
+	@cd ../../../.. ; \
+	echo $(OBJECTNAME) ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]*;  \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.*; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]* ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) 
+
+distribute-all:
+	@cd ../../../.. ; \
+	echo $(OBJECTNAME) ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]*;  \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.*; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]* ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) 
+
+include Config/Target.inc
+
diff --git a/src/Objects/General/eosBayes/doc/.eosBayes.html b/src/Objects/General/eosBayes/doc/.eosBayes.html
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Objects/General/eosBayes/doc/.footer b/src/Objects/General/eosBayes/doc/.footer
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Objects/General/eosBayes/doc/.header b/src/Objects/General/eosBayes/doc/.header
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Objects/General/eosBayes/doc/Makefile b/src/Objects/General/eosBayes/doc/Makefile
new file mode 100755
index 0000000000..11b3c90289
--- /dev/null
+++ b/src/Objects/General/eosBayes/doc/Makefile
@@ -0,0 +1,41 @@
+include ../../../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+
+SOURCEDOC  = $(OBJECTNAME).html
+DOCDSTDIR  = $(EOS_HOME)/doc/Objects
+TARGETDOC  = $(DOCDSTDIR)/$(SOURCEDOC)
+
+all: $(SOURCEDOC)
+
+install : $(TARGETDOC) 
+
+$(TARGETDOC):$(SOURCEDOC)
+	$(INSTALL) -m 444 *.html $(DOCDSTDIR)
+	@cd $(DOCDSTDIR); make
+
+$(SOURCEDOC) : .$(SOURCEDOC) .header .footer ../inc/$(OBJECTNAME).h Makefile ../src/*.c
+	@echo Creating $(OBJECTNAME).html
+	@cat .header	 			 > $(SOURCEDOC)
+	@#htmlUpdateTime 			>> $(SOURCEDOC)
+	@cat .$(SOURCEDOC) 			>> $(SOURCEDOC)
+	@echo \<HR\>  				>> $(SOURCEDOC)
+	@echo "<A NAME=\"Information\">" >> $(SOURCEDOC)
+	@echo "<H2>Information from source codes</H2>" >> $(SOURCEDOC)
+	@echo "</A>"               >> $(SOURCEDOC)
+	@echo "<PRE>"               >> $(SOURCEDOC)
+	-@ident ../src/*.c  			>> $(SOURCEDOC)
+	@echo "</PRE>"              >> $(SOURCEDOC)
+	@echo \<HR\>  				>> $(SOURCEDOC)
+	@echo \<A NAME=\"include\"\>>> $(SOURCEDOC)
+	@echo "<H2>$(OBJECTNAME).h</H2>">> $(SOURCEDOC)
+	@echo \</A\>				>>$(SOURCEDOC)
+	@echo \<PRE\> 				>> $(SOURCEDOC)
+	@cat ../inc/$(OBJECTNAME).h >> $(SOURCEDOC)
+	@echo \</PRE\>				>> $(SOURCEDOC) 
+	@cat .footer				>> $(SOURCEDOC)
+
+clean:
+
+depend:
diff --git a/src/Objects/General/eosBayes/inc/Makefile b/src/Objects/General/eosBayes/inc/Makefile
new file mode 100755
index 0000000000..e1bd97ea2a
--- /dev/null
+++ b/src/Objects/General/eosBayes/inc/Makefile
@@ -0,0 +1,31 @@
+include ../../../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+
+INCFILE = $(OBJECTNAME).h
+
+all: 
+
+install:$(EOS_HOME)/include/$(INCFILE)
+
+$(EOS_HOME)/include/$(INCFILE):$(INCFILE)
+	if [ ! -d  $(EOS_HOME)/include ] ; then \
+		mkdir $(EOS_HOME)/include ; \
+	fi
+	$(INSTALL) -m 444 $(INCFILE) $(EOS_HOME)/include/
+
+clean:
+	$(RM) -f *.bak
+
+depend:
+	$(RM) -f *.bak	
+
+cvsupdate::
+	cvs -d $(EOS_CVSROOT) update 
+
+cvscommit::
+	@echo "cvs -d $(EOS_CVSROOT) commit"  
+
+cvsadd::
+	@echo "cvs -d $(EOS_CVSROOT) add"  
diff --git a/src/Objects/General/eosBayes/inc/eosBayes.h b/src/Objects/General/eosBayes/inc/eosBayes.h
new file mode 100644
index 0000000000..868174ee09
--- /dev/null
+++ b/src/Objects/General/eosBayes/inc/eosBayes.h
@@ -0,0 +1,23 @@
+#ifndef EOS_BAYES_H
+#define EOS_BAYES_H
+
+typedef struct eosBayesDistribution {
+	float min;
+	float max;
+	float delta;
+	int   n;
+	float* prob;
+} eosBayesDistribution;
+
+ 
+typedef struct eosBayes {
+	int numDistribution;
+	eosBayesDistribution* prior;
+	eosBayesDistribution* posterior;
+
+	int numLikelihood;
+	eosBayesDistribution* likelihood;
+} eosBayes;
+
+
+#endif /* EOS_BAYES_H */
diff --git a/src/Objects/General/eosBayes/src/.CCHeader b/src/Objects/General/eosBayes/src/.CCHeader
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Objects/General/eosBayes/src/.CHeader b/src/Objects/General/eosBayes/src/.CHeader
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Objects/General/eosBayes/src/.Ruby b/src/Objects/General/eosBayes/src/.Ruby
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Objects/General/eosBayes/src/.Wish b/src/Objects/General/eosBayes/src/.Wish
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Objects/General/eosBayes/src/Makefile b/src/Objects/General/eosBayes/src/Makefile
new file mode 100755
index 0000000000..7e5dae3249
--- /dev/null
+++ b/src/Objects/General/eosBayes/src/Makefile
@@ -0,0 +1,345 @@
+SHELL=/bin/ksh
+include ../Config/Define.inc
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+
+include $(OSTYPE)/.Source
+include .CHeader
+include .CCHeader
+include .Wish
+include .Ruby
+
+LIBNAME=lib$(OBJECTNAME).a
+SHAREDLIB=lib$(OBJECTNAME).so
+LIBNAMEDEBUG=lib$(OBJECTNAME).debug.a
+
+DSTDIR=../../../../../lib/$(OSTYPE)/
+SOURCE=$(OSTYPE)/.Source
+ARCHTEMPLATEDIR=$(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH
+
+all: hostdepend static-lib shared-lib ruby-lib debug
+	@echo LIBNAME:$(LIBNAME)
+	@echo OBJECTNAME:$(OBJECTNAME)
+
+hostdepend:
+	@if [ ! -L $(OSTYPE) ] ; then  \
+		moveHostdependent ; \
+	fi
+
+debug: debug-lib
+
+static-lib::
+	@echo static-lib:LIBNAME:$(LIBNAME) ; \
+	$(RM) -f $(OSTYPE)/Makefile; \
+	$(CP) $(ARCHTEMPLATEDIR)/Makefile $(OSTYPE)/Makefile ; \
+	cd $(OSTYPE); \
+	$(MAKE) $(LIBNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) WORLDNAME=$(WORLDNAME) 
+
+shared-lib::
+	@echo shared-lib:LIBNAME:$(LIBNAME) ; \
+	$(RM) -f $(OSTYPE)/Makefile;  \
+	$(CP) $(ARCHTEMPLATEDIR)/Makefile $(OSTYPE)/Makefile ; \
+	cd  $(OSTYPE); \
+	$(MAKE) $(SHAREDLIB) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) WORLDNAME=$(WORLDNAME) 
+
+ruby-lib::
+	@if [ -d Swig ]; then \
+		echo "--- Swig ---"; \
+		cd Swig; \
+		if [ -f extconf.rb ] ; then \
+			swig -ruby -I/usr/include -I$(EOS_HOME)/include *.i ; \
+			ruby extconf.rb --with-Eos-include=$(EOS_HOME)/include --with-Eos-lib=$(EOS_HOME)/lib/$(OSTYPE) --with-opt-lib=$LD_LIBRARY_PATH --with-opt-lib=$(EOS_HOME)/util/$(OSTYPE)/lib --with-GL-lib=/usr/lib ; \
+			make ; \
+			make sitearchdir=$(EOS_HOME)/lib/$(OSTYPE) install; \
+		fi ; \
+	fi  
+
+debug-lib::
+	@cd $(OSTYPE); \
+	$(RM) -f Makefile; \
+	$(CP) $(ARCHTEMPLATEDIR)/Makefile Makefile ; \
+	$(MAKE) $(LIBNAMEDEBUG) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) WORLDNAME=$(WORLDNAME) 
+
+clean: 
+	rm -f *.[oa] *.debugo *.cudagdbo *.so *.sharedo *.linkinfo $(OSTYPE)/*.[ao] $(OSTYPE)/*.debugo $(OSTYPE)/*.cudagdbo $(OSTYPE)/*.linkinfo *.bak core $(OSTYPE)/*.sharedo $(OSTYPE)/*.so
+
+Makefile:
+	touch .Source
+	touch .CHeader
+	touch .CCHeader
+
+install: all install-static install-shared install-ascii 
+	@echo "Installation has completed: $(LIBNAME)" 
+
+install-static: $(DSTDIR)/$(LIBNAME)
+install-shared: $(DSTDIR)/$(SHAREDLIB)
+
+install-debug: debug $(DSTDIR)/$(LIBNAMEDEBUG) install-ascii 
+	@echo "Installation has completed: $(LIBNAMEDEBUG)" 
+
+install-ascii: h hh wish ruby 
+
+h:
+	@if [ -n "$(CHeader)" ] ; \
+	then\
+		echo "C Header Install" ; \
+		for file in $(CHeader) dummy ; \
+		do \
+			if [ -f $${file} ] ; \
+			then\
+				echo $${file}; $(INSTALL) -m 444 $${file} $(DSTDIR)/../../include ; \
+			fi;\
+		done; \
+	fi
+
+hh:
+	@if [ -n "$(CCHeader)" ] ; \
+	then \
+		echo "C++ Header Install" ; \
+		for file in $(CCHeader) dummy ; \
+		do \
+			if [ -f $${file} ] ; \
+			then\
+				echo $${file}; $(INSTALL) -m 444 $${file} $(DSTDIR)/../../include ; \
+			fi;\
+		done; \
+	fi
+
+wish:
+	@if [ -n "$(Wish)" ] ; \
+	then \
+		echo "Wish Install" ; \
+		for file in $(Wish) dummy ; \
+		do \
+			if [ -f $${file} ] ; \
+			then\
+				echo $${file}; $(INSTALL) -m 444 $${file} $(DSTDIR)/../../lib ; \
+			fi;\
+		done; \
+	fi
+
+ruby:
+	@if [ -n "$(Ruby)" ] ; \
+	then \
+		echo "Ruby Install" ; \
+		for file in $(Ruby) dummy ; \
+		do \
+			if [ -f $${file} ] ; \
+			then\
+				echo $${file}; $(INSTALL) -m 444 $${file} $(DSTDIR)/../../lib ; \
+			fi;\
+		done; \
+	fi
+
+put:
+	@Files=`ls -l | grep $${USER} | grep rw | grep -e "\.c" ` ;\
+	for file in $${Files} dummy; \
+	do \
+		if [ -w $${file} ] ; \
+		then\
+			echo $${file}; sccsPut $${file} ; \
+		fi;\
+	done
+
+$(DSTDIR)/$(LIBNAME): static-lib
+	@echo Installing lib: $(LIBNAME)
+	@if [ ! -d $(DSTDIR) ] ; then mkdir $(DSTDIR) ; fi
+	@cd $(OSTYPE); $(INSTALL) -m 444 $(LIBNAME) ../$(DSTDIR)
+	@echo LIBNAME:$(LIBNAME)
+	@echo Link EosObjects
+	@OBJLIST=`ls $(OSTYPE)/*.o `;\
+	echo $${OBJLIST} | sed -f ../../../../Config/o2nl.sed > .tmp1 ; \
+	echo $(REALOBJ)  | sed -f ../../../../Config/o2nl.sed > .tmp2 ; \
+	echo "#### Attention Uncompiled file ####";\
+	comm -13 .tmp1 .tmp2 ; \
+	echo "########";\
+	echo $(AR) r $(DSTDIR)/libEosObjects.a $${OBJLIST} ; \
+	$(AR) r $(DSTDIR)/libEosObjects.a $${OBJLIST}; \
+	echo $(AR) s $(DSTDIR)/libEosObjects.a ; \
+	$(AR) s $(DSTDIR)/libEosObjects.a \
+	chmod 660 $(DSTDIR)/libEosObjects.a
+	@rm .tmp1 .tmp2
+
+$(DSTDIR)/$(LIBNAMEDEBUG): debug 
+	@echo Installing lib: $(LIBNAMEDEBUG)
+	@if [ ! -d $(DSTDIR) ] ; then mkdir $(DSTDIR) ; fi
+	@cd $(OSTYPE); $(INSTALL) -m 444 $(LIBNAMEDEBUG) ../$(DSTDIR)
+	@echo LIBNAME:$(LIBNAMEDEBUG)
+	@echo Link EosObjects
+	@OBJLISTDEBUG=`ls $(OSTYPE)/*.debugo `;\
+	echo $${OBJLISTDEBUG} | sed -f ../../../../Config/o2nl.sed > .tmp1 ; \
+	echo $(REALOBJDEBUG)  | sed -f ../../../../Config/o2nl.sed > .tmp2 ; \
+	echo "#### Attention Uncompiled file ####";\
+	comm -13 .tmp1 .tmp2 ; \
+	echo "########";\
+	echo $(AR) r $(DSTDIR)/libEosObjects.debug.a $${OBJLISTDEBUG} ; \
+	$(AR) r $(DSTDIR)/libEosObjects.debug.a $${OBJLISTDEBUG}; 
+	echo $(AR) s $(DSTDIR)/libEosObjects.debug.a ; \
+	$(AR) s $(DSTDIR)/libEosObjects.debug.a 
+	chmod 660 $(DSTDIR)/libEosObjects.debug.a
+	@rm .tmp1 .tmp2
+
+$(DSTDIR)/$(SHAREDLIB): shared-lib
+	@echo Installing lib: $(SHAREDLIB)
+	@if [ ! -d $(DSTDIR) ] ; then mkdir $(DSTDIR) ; fi
+	@cd $(OSTYPE); $(INSTALL) -m 444 $(SHAREDLIB) ../$(DSTDIR)
+	@echo LIBNAME:$(SHAREDLIB)
+	@echo Link EosObjects
+	@OBJLIST=`ls $(OSTYPE)/*.sharedo `;\
+	echo $${OBJLIST} | sed -f ../../../../Config/o2nl.sed > .tmp1 ; \
+	echo $(REALSHAREDOBJ)  | sed -f ../../../../Config/o2nl.sed > .tmp2 ; \
+	echo "#### Attention Uncompiled file ####";\
+	comm -13 .tmp1 .tmp2 ; \
+	echo "########"; \
+	if [ ! -d  $(DSTDIR)/shared ] ; then \
+		mkdir $(DSTDIR)/shared; \
+	fi; \
+	$(CP) $${OBJLIST} $(DSTDIR)/shared ; \
+	echo "$(CP) $${OBJLIST} $(DSTDIR)/shared" ; \
+	$(SHARED) $(DSTDIR)/libEosObjects.so $(DSTDIR)/shared/*.sharedo ; \
+	echo "$(SHARED) $(DSTDIR)/libEosObjects.so $(DSTDIR)/shared/*.sharedo" ; \
+	chmod 660 $(DSTDIR)/libEosObjects.so
+	@rm .tmp1 .tmp2
+
+install-all: 
+	@cd ..  ; $(MAKE) install
+
+install-ruby: ruby-lib
+	cd $(OSTYPE); $(RUBY) -r ftools -e 'File::install(ARGV[0], ARGV[1], 0555, true)' $(SHAREDLIB) $(RUBYSHAREDLIB)/$(SHAREDLIB)	
+
+depend:
+	@echo dependency checking now 
+	@echo $(OSTYPE)
+	@echo SRC = \\ > $(SOURCE) 
+	@ls -1 *.c  | sed -e "s/\.c/.c \\\\/"   >> $(SOURCE)
+	@ls -1 *.cc | sed -e "s/\.cc/.cc \\\\/" >> $(SOURCE)
+	@ls -1 *.ccm | sed -e "s/\.ccm/.ccm \\\\/" >> $(SOURCE)
+	@ls -1 *.idl | sed -e "s/\.idl/.idl \\\\/" >> $(SOURCE)
+	@ls -1 *.cu | sed -e "s/\.cu/.cu \\\\/" >> $(SOURCE)
+	@echo >> $(SOURCE)
+	@#
+	@echo OBJ = \\ >> $(SOURCE)
+	@ls -1 *.c   | sed -e "s/\.c/.o \\\\/"    >> $(SOURCE)
+	@ls -1 *.cc  | sed -e "s/\.cc/.o  \\\\/"  >> $(SOURCE)
+	@ls -1 *.ccm  | sed -e "s/\.ccm/.o  \\\\/"  >> $(SOURCE)
+	@ls -1 *.idl | sed -e "s/\.idl/.o  \\\\/" >> $(SOURCE)
+	@ls -1 *.cu  | sed -e "s/\.cu/.o  \\\\/"  >> $(SOURCE)
+	@echo >> $(SOURCE)
+	@#
+	@echo SHAREDOBJ = \\ >> $(SOURCE)
+	@ls -1 *.c   | sed -e "s/\.c/.sharedo \\\\/"    >> $(SOURCE)
+	@ls -1 *.cc  | sed -e "s/\.cc/.sharedo  \\\\/"  >> $(SOURCE)
+	@ls -1 *.ccm  | sed -e "s/\.ccm/.sharedo  \\\\/"  >> $(SOURCE)
+	@ls -1 *.idl | sed -e "s/\.idl/.sharedo  \\\\/" >> $(SOURCE)
+	@ls -1 *.cu  | sed -e "s/\.cu/.sharedo  \\\\/"  >> $(SOURCE)
+	@echo >> $(SOURCE)
+	@#
+	@echo REALOBJ = \\ >> $(SOURCE)
+	@ls -1 *.c   | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.c/.o \\\\/"  >> $(SOURCE)
+	@ls -1 *.cc  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cc/.o \\\\/" >> $(SOURCE)
+	@ls -1 *.ccm  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.ccm/.o \\\\/" >> $(SOURCE)
+	@ls -1 *.idl | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.idl/.o \\\\/" >> $(SOURCE)
+	@ls -1 *.cu  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cu/.o \\\\/" >> $(SOURCE)
+	@echo >> $(SOURCE) 
+	@echo REALSHAREDOBJ = \\ >> $(SOURCE)
+	@ls -1 *.c   | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.c/.sharedo \\\\/"  >> $(SOURCE)
+	@ls -1 *.cc  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cc/.sharedo \\\\/" >> $(SOURCE)
+	@ls -1 *.ccm  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.ccm/.sharedo \\\\/" >> $(SOURCE)
+	@ls -1 *.idl | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.idl/.sharedo \\\\/" >> $(SOURCE)
+	@ls -1 *.cu  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cu/.sharedo \\\\/" >> $(SOURCE)
+	@echo >> $(SOURCE) 
+	@echo OBJDEBUG = \\ >> $(SOURCE)
+	@ls -1 *.c   | sed -e "s/\.c/.debugo \\\\/"    >> $(SOURCE)
+	@ls -1 *.cc  | sed -e "s/\.cc/.debugo  \\\\/"  >> $(SOURCE)
+	@ls -1 *.ccm  | sed -e "s/\.ccm/.debugo  \\\\/"  >> $(SOURCE)
+	@ls -1 *.idl | sed -e "s/\.idl/.debugo  \\\\/" >> $(SOURCE)
+	@echo >> $(SOURCE)
+	@#
+	@echo REALOBJDEBUG = \\ >> $(SOURCE)
+	@ls -1 *.c   | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.c/.debugo \\\\/"  >> $(SOURCE)
+	@ls -1 *.cc  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cc/.debugo \\\\/" >> $(SOURCE)
+	@ls -1 *.ccm  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.ccm/.debugo \\\\/" >> $(SOURCE)
+	@ls -1 *.idl | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.idl/.debugo \\\\/" >> $(SOURCE)
+	@ls -1 *.cu  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cu/.debugo \\\\/" >> $(SOURCE)
+	@echo >> $(SOURCE) 
+	@echo OBJCUDAGDB = \\ >> $(SOURCE)
+	@ls -1 *.c   | sed -e "s/\.c/.cudagdb.o \\\\/"    >> $(SOURCE)
+	@ls -1 *.cc  | sed -e "s/\.cc/.cudagdb.o  \\\\/"  >> $(SOURCE)
+	@ls -1 *.cu  | sed -e "s/\.cu/.cudagdb.o  \\\\/"  >> $(SOURCE)
+	@echo >> $(SOURCE)
+	@#
+	@echo REALOBJCUDAGDB = \\ >> $(SOURCE)
+	@ls -1 *.c   | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.c/.cudagdb.o \\\\/"  >> $(SOURCE)
+	@ls -1 *.cc  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cc/.cudagdb.o \\\\/" >> $(SOURCE)
+	@ls -1 *.cu  | sed -e "s/^/\$(OSTYPE)\//" -e "s/\.cu/.cudagdb.o \\\\/" >> $(SOURCE)
+	@echo >> $(SOURCE) 
+	@#
+	@echo >> $(SOURCE)
+	@echo CCHeader = \\ > .CCHeader
+	@ls -1 *.hh | sed -e "s/\.hh/.hh \\\\/" >> .CCHeader
+	@echo >> .CCHeader
+	@#
+	@echo CHeader = \\ > .CHeader
+	@ls -1 *.h | sed -e "s/\.h/.h \\\\/" >> .CHeader
+	@echo >> .CHeader
+	@#
+	@echo Wish = \\ > .Wish
+	@ls -1 *.wish | sed -e "s/\.wish/.wish \\\\/" >> .Wish
+	@echo >> .Wish
+	@#
+	@echo Ruby = \\ > .Ruby
+	@ls -1 *.rb | sed -e "s/\.rb/.rb \\\\/" >> .Ruby
+	@echo >> .Ruby
+	@#
+	@ls -1 *.c *.cc *.ccm | \
+	awk -vHostType=$(OSTYPE) -f$(EOS_HOME)/sbin/awk/objectdependency.awk > $(OSTYPE)/.Depend
+	@#
+	@$(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(KHOROS_INCS) *.c *.cc *.ccm >> $(OSTYPE)/.Depend
+	@for file in $(SRC) dummy ; \
+	do  \
+		if [ -f $${file} ] ; \
+		then \
+			echo $${file} ; \
+			ln -sf ../$${file} $(OSTYPE)/$${file}; \
+		fi ;\
+	done
+
+#
+#
+#
+test::
+	@if [ -d test ] ; then \
+		cd test; \
+		$(MAKE); \
+	else \
+		echo "No test directory: making test"; \
+		mkdir test; \
+		cd test; \
+		touch Makefile; \
+	fi
+
+#
+# cvs
+#
+cvsupdate::
+	cvs -d $(EOS_CVSROOT) update -d 
+
+cvslogin::
+	cvs -d $(EOS_CVSROOT) login 
+
+cvscommit::
+	@echo "cvs -d $(EOS_CVSROOT) commit -m @"message@" filename"
+
+cvsadd::
+	@echo "cvs -d $(EOS_CVSROOT) add  filename|dirname"
+	@echo "Need Commit for filename"
+	@echo "make cvscommit"
+
+cvsremove::
+	@echo "cvs -d $(EOS_CVSROOT) remove filename"
+	@echo "Need Commit for filename"
+	@echo "make cvscommit" 
+
+include $(OSTYPE)/.Depend
+include ../Config/Target.inc
diff --git a/src/Objects/General/eosBayes/src/X86MAC64 b/src/Objects/General/eosBayes/src/X86MAC64
new file mode 120000
index 0000000000..dfa64e5043
--- /dev/null
+++ b/src/Objects/General/eosBayes/src/X86MAC64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86MAC64/src/Objects/General/eosBayes/src/X86MAC64
\ No newline at end of file
diff --git a/src/Objects/Makefile b/src/Objects/Makefile
old mode 100755
new mode 100644
diff --git a/src/Objects/Makefile.org b/src/Objects/Makefile.org
new file mode 100755
index 0000000000..ad841104b1
--- /dev/null
+++ b/src/Objects/Makefile.org
@@ -0,0 +1,5 @@
+include ../Config/Define.inc
+include Config/Define.inc
+include .Source
+
+include Config/Target.inc
diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index 67934f8342..eb66cdbb70 100755
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -586,3 +586,12 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
diff --git a/src/Tools/mrcImage/.Source b/src/Tools/mrcImage/.Source
index ec4753832a..ef79cce4ca 100644
--- a/src/Tools/mrcImage/.Source
+++ b/src/Tools/mrcImage/.Source
@@ -34,6 +34,7 @@ mrcImage2pdb \
 mrcImage3DHighResoEmphasis \
 mrcImage3DPad \
 mrcImage3DPad2 \
+mrcImage3DPeakGet \
 mrcImage3DSymmetryFind \
 mrcImage3DWindowing \
 mrcImageAbnormalValueRemove \
@@ -203,6 +204,7 @@ mrcImageReverse \
 mrcImageRotation \
 mrcImageRotation3D \
 mrcImageSN \
+mrcImageSNEstimate \
 mrcImageSamplingUnitChange \
 mrcImageScalarAdd \
 mrcImageSectionGet \
diff --git a/src/Tools/mrcImage/.Source.org b/src/Tools/mrcImage/.Source.org
index 9452085064..2b2774e3b7 100644
--- a/src/Tools/mrcImage/.Source.org
+++ b/src/Tools/mrcImage/.Source.org
@@ -34,6 +34,7 @@ mrcImage2pdb \
 mrcImage3DHighResoEmphasis \
 mrcImage3DPad \
 mrcImage3DPad2 \
+mrcImage3DPeakGet \
 mrcImage3DSymmetryFind \
 mrcImage3DWindowing \
 mrcImageAbnormalValueRemove \
@@ -137,6 +138,7 @@ mrcImageHoughTransform \
 mrcImageHoughTransformInverse \
 mrcImageInfo \
 mrcImageLabeling \
+mrcImageLocalMaximumValuesFind \
 mrcImageLogicalOperation \
 mrcImageLowPassFilter \
 mrcImageMagnificationChange \
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/Config/Define.inc b/src/Tools/mrcImage/mrcImage3DPeakGet/Config/Define.inc
new file mode 100755
index 0000000000..263a4e117b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/Config/Define.inc
@@ -0,0 +1,4 @@
+OBJECTNAME = mrcImage3DPeakGet
+EXTRA_LIB  =
+EXTRA_CCOPTS =
+EXTRA_INC =
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/Config/OptionControlFile b/src/Tools/mrcImage/mrcImage3DPeakGet/Config/OptionControlFile
new file mode 100755
index 0000000000..187cd32ffb
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/Config/OptionControlFile
@@ -0,0 +1,7 @@
+# OptionControlFile
+# FileFormat
+"-i","-i[nput]","Input:3D","Essential","1","1","In","inFile::mrcImage","NULL"
+"-I","-I[nformation]","Input:ROI Info","Optional","1","1","Info","inFile::ASCII","stdin"
+"-o","-o[utput]","Output:Positon","Optional","1","1","Out","outFile::ASCII","stdout"
+"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
+"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/Config/Target.inc b/src/Tools/mrcImage/mrcImage3DPeakGet/Config/Target.inc
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/Makefile b/src/Tools/mrcImage/mrcImage3DPeakGet/Makefile
new file mode 100755
index 0000000000..6c4a33690a
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/Makefile
@@ -0,0 +1,115 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+	cd src; make all; cd ..
+
+install:
+	cd src; make install; cd ..
+
+
+putSF:
+	if [ -f private ] ; \
+	then \
+		echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+	else \
+		cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+	fi
+
+put:
+	cd src; make put; cd ..
+
+clean:
+	cd src; make clean; cd ..
+
+depend:
+	cd src; make depend; cd ..
+
+check:
+	@if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+		echo making directory; \
+		mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+	fi
+	ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+	@$(RM) src/Makefile
+	@echo "New src/Makefile" 
+	@$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+	@cd src; touch $(OSTYPE)/.Depend; make depend
+
+update:
+	@if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+		echo making directory; \
+		mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+	fi
+	ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+	@$(RM) src/Makefile
+	@echo "New src/Makefile" 
+	@$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+	@cd src; touch $(OSTYPE)/.Depend; echo "Y" | make update      
+
+cvsupdate::
+	cvs -d $(EOS_CVSROOT) update -d 
+
+cvscommit::
+	cvs -d $(EOS_CVSROOT) commit
+
+backup:
+	@cd ../../../..;     \
+	echo $(OBJECTNAME) ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config	; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+	@cd ../../../..;     \
+	echo $(OBJECTNAME) ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config	; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+	
+distribute:
+	cd ../../../..;     \
+	echo $(OBJECTNAME) ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config	; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+	
+distribute-all:
+	@cd ../../../..;     \
+	echo $(OBJECTNAME) ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config	; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+	${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
+
+include Config/Target.inc
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/doc/Makefile b/src/Tools/mrcImage/mrcImage3DPeakGet/doc/Makefile
new file mode 100755
index 0000000000..8215199e1b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/doc/Makefile
@@ -0,0 +1,2 @@
+install:
+	cd ../src; make install-doc; cd ../doc	
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/inc/config.h b/src/Tools/mrcImage/mrcImage3DPeakGet/inc/config.h
new file mode 100755
index 0000000000..f653f36e8b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/inc/config.h
@@ -0,0 +1,6 @@
+#ifndef CONFIG_H
+#define CONFIG_H
+
+#include "../inc/mrcImage3DPeakGet.h"
+
+#endif /* CONFIG_H */
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/inc/mrcImage3DPeakGet.h b/src/Tools/mrcImage/mrcImage3DPeakGet/inc/mrcImage3DPeakGet.h
new file mode 100755
index 0000000000..c205bb1e34
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/inc/mrcImage3DPeakGet.h
@@ -0,0 +1,50 @@
+#ifndef MRCIMAGE3DPEAKGET_H
+#define MRCIMAGE3DPEAKGET_H
+#include <stdio.h>
+#include <stdlib.h>
+
+#define OPTION_FLAG     '-'
+#define OPTION_FLAG_POS (0)
+#define OPTION_POS      (1)
+
+
+
+
+typedef struct mrcImage3DPeakGetInfo {
+    long flagRedirect;
+
+    long flagIn;
+    char* In;
+    FILE* fptIn;
+    
+    long flagInfo;
+    char* Info;
+    FILE* fptInfo;
+    
+    long flagOut;
+    char* Out;
+    FILE* fptOut;
+    
+    long flagconfigFile;
+    char* configFile;
+    FILE* fptconfigFile;
+    
+    long flagmode;
+    long mode;
+    
+} mrcImage3DPeakGetInfo;
+#ifdef __cplusplus
+extern "C" {
+#endif
+extern void argCheck(mrcImage3DPeakGetInfo* info, int argc, char* avgv[]);
+extern void khorosInit(int argc, char* avgv[]);
+extern void init0(mrcImage3DPeakGetInfo* info);
+extern void init1(mrcImage3DPeakGetInfo* info);
+extern void usage(char* usage);
+extern void additionalUsage(void);
+extern void htmlBeforeUsage(char* usage);
+extern void htmlAfterUsage(char* usage);
+#ifdef __cplusplus
+};
+#endif
+#endif /* MRCIMAGE3DPEAKGET_H */
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/.Depend b/src/Tools/mrcImage/mrcImage3DPeakGet/src/.Depend
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/.Source b/src/Tools/mrcImage/mrcImage3DPeakGet/src/.Source
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/Makefile b/src/Tools/mrcImage/mrcImage3DPeakGet/src/Makefile
new file mode 100755
index 0000000000..7beb110976
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/Makefile
@@ -0,0 +1,427 @@
+include ../Config/Define.inc
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+
+EOSHOME=../../../../../
+DSTDIR=$(EOSHOME)/bin
+DSTDOC=$(EOSHOME)/doc
+DSTTAR=$(EOSHOME)/tar
+
+INCFILES   = 
+
+LIBFILES   = \
+			$(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+			$(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+			$(OBJECTNAME).c \
+			init.c \
+			argCheck.c \
+			usage.c  \
+			util.c \
+
+SRCCXX  = \
+			$(OBJECTNAME).cc \
+			init.cc \
+			argCheck.cc \
+			usage.cc  \
+			util.cc \
+
+MODULES    = \
+			$(OBJECTNAME).o \
+			init.o \
+			argCheck.o \
+			usage.o  \
+			util.o \
+
+REALMODULES    = \
+			$(OSTYPE)/$(OBJECTNAME).o \
+			$(OSTYPE)/init.o \
+			$(OSTYPE)/argCheck.o \
+			$(OSTYPE)/usage.o \
+			$(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+			$(OBJECTNAME).debugo \
+			init.debugo \
+			argCheck.debugo \
+			usage.debugo  \
+			util.debugo \
+
+REALMODULESDEBUG    = \
+			$(OSTYPE)/$(OBJECTNAME).debugo \
+			$(OSTYPE)/init.debugo \
+			$(OSTYPE)/argCheck.debugo \
+			$(OSTYPE)/usage.debugo \
+			$(OSTYPE)/util.debugo 
+
+
+all: $(OSTYPE)/$(OBJECTNAME) 
+	if [ ! -L $(OSTYPE) ] ; then \
+		moveHostdependent; \
+	fi
+
+debug: $(OSTYPE)/$(OBJECTNAME).debug
+
+cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb
+
+
+$(OSTYPE)/$(OBJECTNAME)::
+	@$(RM) -f $(OSTYPE)/Makefile ; \
+	$(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+	cd $(OSTYPE); \
+	$(MAKE) $(OBJECTNAME)  WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+$(OSTYPE)/$(OBJECTNAME).debug::
+	@$(RM) -f $(OSTYPE)/Makefile ; \
+	$(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+	cd $(OSTYPE); \
+	$(MAKE) $(OBJECTNAME).debug  WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+$(OSTYPE)/$(OBJECTNAME).cudagdb::
+	@$(RM) -f $(OSTYPE)/Makefile ; \
+	$(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+	cd $(OSTYPE); \
+	$(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+cvsupdate::
+	cvs -d $(EOS_CVSROOT) update -d	
+
+cvscommit::
+	cvs -d $(EOS_CVSROOT) commit 
+
+edit:
+	@if [ -r $(OBJECTNAME).c ]; \
+	then \
+		sccsEdit $(OBJECTNAME).c; \
+	else \
+		echo "Source files are already editable"; \
+	fi
+	@if [ -r wish/$(OBJECTNAME).wish ]; \
+	then \
+		cd wish; sccsEdit $(OBJECTNAME).wish; \
+	else \
+		echo "Source files (wish) are already editable."; \
+	fi
+	@if [ -r ruby/$(OBJECTNAME).rb ]; \
+	then \
+		cd ruby; sccsEdit $(OBJECTNAME).rb; \
+	else \
+		echo "Source files (ruby) are already editable."; \
+	fi
+	@if [ -r perl/$(OBJECTNAME).pl ]; \
+	then \
+		cd perl; sccsEdit $(OBJECTNAME).pl ; \
+	else \
+		echo "Source files (perl) are already editable."; \
+	fi
+	@if [ -r ../Config/OptionControlFile ]; \
+	then \
+		cd ../Config; sccsEdit OptionControlFile; \
+	else \
+		echo "OptionControlFile are already editable."; \
+	fi
+	
+unedit:
+	@if [ -w $(OBJECTNAME).c ]; \
+	then \
+		sccsUnedit $(OBJECTNAME).c; \
+	else \
+		echo "Source files are not editable"; \
+	fi
+	@if [ -w wish/$(OBJECTNAME).wish ]; \
+	then \
+		cd wish; sccsUnedit $(OBJECTNAME).wish; \
+	else \
+		echo "Source files (wish) are not editable."; \
+	fi
+	@if [ -w ruby/$(OBJECTNAME).rb]; \
+	then \
+		cd ruby; sccsUnedit $(OBJECTNAME).rb; \
+	else \
+		echo "Source files (ruby) are not editable."; \
+	fi
+	@if [ -w perl/$(OBJECTNAME).pl ]; \
+	then \
+		cd perl; sccsUnedit $(OBJECTNAME).pl ; \
+	else \
+		echo "Source files (ruby) are not editable."; \
+	fi
+	@if [ -w ../Config/OptionControlFile ]; \
+	then \
+		cd ../Config; sccsUnedit OptionControlFile; \
+	else \
+		echo "OptionControlFile are not editable."; \
+	fi
+	
+report:
+	@if [ -r $(OBJECTNAME).c ]; \
+	then \
+		sccsReport $(OBJECTNAME).c; \
+	else \
+		echo "Source files are already editable"; \
+	fi
+	@if [ -r wish/$(OBJECTNAME).wish ]; \
+	then \
+		cd wish; sccsReport $(OBJECTNAME).wish; \
+	else \
+		echo "Source files (wish) are already editable."; \
+	fi
+	@if [ -r ruby/$(OBJECTNAME).rb ]; \
+	then \
+		cd ruby; sccsReport $(OBJECTNAME).rb; \
+	else \
+		echo "Source files (ruby) are already editable."; \
+	fi
+	@if [ -r perl/$(OBJECTNAME).pl ] ; \
+	then \
+		cd perl; sccsReport $(OBJECTNAME).pl ; \
+	else \
+		echo "Source files (perl) are already editable."; \
+	fi
+	@if [ -r ../Config/OptionControlFile ]; \
+	then \
+		cd ../Config; sccsReport OptionControlFile; \
+	else \
+		echo "OptionControlFile are already editable."; \
+	fi
+
+clean : 
+	rm -f *.debugo $(OSTYPE)/*.debugo *.cudagdbo $(OSTYPE)/*.cudagdbo *.o $(OSTYPE)/*.o *.linkinfo $(OSTYPE)/*.linkinfo \
+		$(OSTYPE)/$(OBJECTNAME) $(OSTYPE)/*.$(OSTYPE) \
+		$(OSTYPE)/$(OBJECTNAME).debug $(OSTYPE)/*.$(OSTYPE).debug \
+		$(OSTYPE)/$(OBJECTNAME).cudagdb $(OSTYPE)/*.$(OSTYPE).cudagdb \
+		$(OSTYPE)/$(OBJECTNAME).linkinfo $(OSTYPE)/*.$(OSTYPE).linkinfo \
+		*.bak *.$(OSTYPE) core
+
+install: install-bin install-doc install-wish install-ruby install-shell install-perl
+	@if [ dummy$(KHOROS_KENGOBJ) != dummy ]  ; \
+	then \
+		if [ -x $(KHOROS_KGENOBJ) ] ;  \
+		then \
+			make install-khoros ; \
+		fi; \
+	fi 
+
+install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) 
+
+$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME) 
+	@echo ---- Installing to bin
+	@echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
+	@if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \
+	then \
+		mkdir $(DSTDIR)/$(OSTYPE); \
+	fi
+	@if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
+	then \
+		echo "Compilation is complete"; \
+		$(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+		$(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
+		$(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+	else \
+		echo "Compilation is incomplete. $(OBJECTNAME)"; \
+	fi
+	@echo ---- end of bin
+
+install-wish:
+	@if [ -d wish ]; \
+	then \
+		echo "---- Tcl/Tk file Install"; \
+		if [ ! -d $(DSTDIR)/wish/$(OBJECTNAME) ]; \
+		then \
+			mkdir $(DSTDIR)/wish/$(OBJECTNAME) ; \
+		fi ; \
+		$(CP) -f wish/* $(DSTDIR)/wish/$(OBJECTNAME); \
+		$(CHMOD) 555 $(DSTDIR)/wish/$(OBJECTNAME)/*  ;\
+		touch $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
+		$(CHMOD) 666 $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
+		echo "---- Tcl/Tk file Installed";\
+	fi
+
+install-ruby:
+	@if [ -d ruby ]; \
+	then \
+		echo "---- Ruby/Tk file Install"; \
+		if [ ! -d $(DSTDIR)/ruby/$(OBJECTNAME) ]; \
+		then \
+			mkdir $(DSTDIR)/ruby/$(OBJECTNAME) ; \
+		fi ; \
+		$(CP) -f ruby/* $(DSTDIR)/ruby/$(OBJECTNAME); \
+		$(CHMOD) 555 $(DSTDIR)/ruby/$(OBJECTNAME)/* ; \
+		echo "---- Ruby/Tk file Installed"; \
+	fi
+
+install-perl:
+	@if [ -d perl ]; \
+	then \
+		echo "---- Perl/Tk file Install"; \
+		if [ ! -d $(DSTDIR)/perl/$(OBJECTNAME) ]; \
+		then \
+			mkdir $(DSTDIR)/perl/$(OBJECTNAME) ; \
+		fi; \
+		$(CP) -f perl/* $(DSTDIR)/perl/$(OBJECTNAME); \
+		$(CHMOD) 555 $(DSTDIR)/perl/$(OBJECTNAME)/* ; \
+		echo "---- Perl/Tk file Installed"; \
+	fi
+
+install-shell:
+	@if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
+	then \
+		mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
+	fi
+	@if [ -d shell ]; \
+	then \
+		echo "---- Shell file Install"; \
+		if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
+		then \
+			mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
+		fi ; \
+		$(CP) -f shell/* $(DSTDIR)/shell/$(OBJECTNAME); \
+		$(CHMOD) 555 $(DSTDIR)/shell/$(OBJECTNAME)/*; \
+		echo "---- Shell file Installed"; \
+	fi
+
+install-khoros:
+	@echo Installing to khoros
+	@if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KGENOBJ) ]; \
+	then \
+		echo kgenobj;\
+		$(KHOROS_KGENOBJ) -tb Eos -oname $(OBJECTNAME) -type script -pane -cantata true -cat Eos -subcat $(CLASSNAME) -description $(OBJECTNAME) -bname $(OBJECTNAME) -form  -lang ksh ; \
+	fi
+	@if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
+	then \
+		$(KHOROS_KSET) -tb Eos -oname $(OBJECTNAME) -icon $(OBJECTNAME) ; \
+	fi
+	@if [ -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
+	then \
+		$(CHMOD) -R 775 ../../../../../objects/script/$(OBJECTNAME) ; \
+		if [ $?  ] ; \
+		then \
+			echo "-- setting khoros ---" ; \
+			if [ -d ../../../../../objects/script/$(OBJECTNAME)/uis/ ] ; \
+			then \
+				$(CD) ../../../../../objects/script/$(OBJECTNAME)/uis/ ; \
+				$(RM) -f $(OBJECTNAME).pane ; \
+				$(LN) -s ../../../../src/Tools/$(CLASSNAME)/$(OBJECTNAME)/src/$(OBJECTNAME).pane $(OBJECTNAME).pane; \
+				$(CD) ../../ ; \
+				$(CHMOD) -R 555 $(OBJECTNAME); \
+			else \
+				echo "../../../../../objects/script/$(OBJECTNAME)/uis/ does not exist."; \
+			fi ; \
+		else \
+			echo "Failed !!: Cannot chage mode in installing  $(OBJECTNAME) to khoros system"; \
+		fi ; \
+		echo "-- end of khoros-installing"; \
+	fi
+
+install-doc: html 
+	@if [ ! -d $(DSTDOC)/SmallTools ]; \
+	then \
+		mkdir $(DSTDOC)/SmallTools ;\
+	fi
+	@if [ -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ]; \
+	then \
+		$(RM) -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ;\
+	fi
+	@$(CP) $(OBJECTNAME).html  $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+	@$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+	@if [ -f ../doc/*.html ]; \
+	then \
+		$(CP) ../doc/*.html  $(DSTDOC)/SmallTools/ ;\
+	fi
+	@$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+	@if [ -f $(DSTDOC)/SmallTools/Makefile ]; \
+	then \
+		cd $(DSTDOC)/SmallTools; $(MAKE); \
+	fi
+
+html: $(OBJECTNAME).html
+
+configFileRead:
+	@ctrl2configFileRead $(CLASSNAME) $(OBJECTNAME) ../Config/OptionControlFile
+
+$(OBJECTNAME).html: $(OSTYPE)/$(OBJECTNAME)
+	@echo creating html
+	@$(OSTYPE)/$(OBJECTNAME) -html 2> $(OBJECTNAME).html.tmp
+	@sed -e s/$(OSTYPE)\\/// $(OBJECTNAME).html.tmp > $(OBJECTNAME).html
+	@$(RM) $(OBJECTNAME).html.tmp
+
+$(DSTDIR)/$(OBJECTNAME): $(OSTYPE)/$(OBJECTNAME)
+	@ln -s -f ../sbin/MachineIndependent $@
+
+depend::
+	@echo dependency checking now
+	@if [ ! -L $(OSTYPE) ] ; then \
+		moveHostdependent; \
+	fi
+	rm -f $(OSTYPE)/.Depend	
+	#echo C
+	@if [ -f $(OBJECTNAME).c ] ; \
+	then \
+		echo "dependency: *.c"; \
+		echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c   ; \
+		     $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c                  >> $(OSTYPE)/.Depend ; \
+	fi
+	#echo CC
+	@if [ -f $(OBJECTNAME).cc ] ; \
+	then \
+		echo "dependency: *.cc"; \
+		echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc ; \
+		     $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc >> $(OSTYPE)/.Depend ; \
+	fi
+	@if [ -f $(OBJECTNAME).ccm ] ; \
+	then \
+		echo "dependency: *.ccm"; \
+		echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm ; \
+		     $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm >> $(OSTYPE)/.Depend ; \
+	fi
+	@if [ -f $(OBJECTNAME).cu ] ; \
+	then \
+		echo "dependency: *.cu"; \
+		echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu ; \
+		     $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu >> $(OSTYPE)/.Depend ; \
+	fi
+
+update:../Config/OptionControlFile
+	maketool $(CLASSNAME) $(OBJECTNAME) update
+
+changeName::
+
+Test:$(OSTYPE)/$(OBJECTNAME) TestDir
+	@if [ -f test/Makefile ] ; \
+	then \
+		cd test; make ; \
+	else \
+		echo "No test Makefile"; \
+	fi
+
+TestDir::
+	@if [ ! -d test ] ; \
+	then \
+		echo "Creating test dir"; \
+		mkdir  test; \
+	fi
+	@if [ ! -f test/Makefile ] ; \
+	then \
+		echo "Creating Makefile"; \
+		cd test; \
+		protoTestMakefileCreate; \
+	fi
+	@if [ ! -d test/data ]; \
+	then \
+		mkdir $(EOSHOME)/data/$(OBJECTNAME); \
+		cd test; \
+		ln -sf ../$(EOSHOME)/data/$(OBJECTNAME) data; \
+	fi 
+
+tar::
+	cd $(DSTTAR); tar cvf Tools.$(CLASSNAME).$(OBJECTNAME).tar ../bin/$(OBJECTNAME) \
+	                                                     ../bin/*/$(OBJECTNAME).* \
+	                                                     ../src/Tools/$(CLASSNAME)/$(OBJECTNAME) \
+				; gzip Tools.$(CLASSNAME).$(OBJECTNAME).tar
+
+-include $(OSTYPE)/.Depend
+-include ../Config/Target.inc
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/X86MAC64 b/src/Tools/mrcImage/mrcImage3DPeakGet/src/X86MAC64
new file mode 120000
index 0000000000..ea0806dff8
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/X86MAC64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImage3DPeakGet/src/X86MAC64
\ No newline at end of file
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/argCheck.c b/src/Tools/mrcImage/mrcImage3DPeakGet/src/argCheck.c
new file mode 100755
index 0000000000..5e89a55a03
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/argCheck.c
@@ -0,0 +1,107 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "../inc/config.h"
+#include "genUtil.h"
+#include "String.h"
+#include "File.h"
+#include "Memory.h"
+
+
+void
+argCheck(mrcImage3DPeakGetInfo* info, int argc, char* argv[])
+{
+    long i;
+    char s[1024];
+    FILE* fpt;
+    
+    if(NULL==(fpt=fopen(".EosLog", "a+"))) { 
+        
+    } else {
+        for(i=0; i<argc; i++) {
+            fprintf(fpt, "%s ", argv[i]);
+        }
+        fprintf(fpt, "\n");
+        fclose(fpt);
+    }
+    for(i=1; i<argc; i++) {
+        if(OPTION_FLAG==argv[i][OPTION_FLAG_POS]) {
+            SSWITCH(argv[i]+OPTION_POS)
+                SCASE("i") {
+                    if(i+1<argc) {
+                        info->In = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagIn++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("I") {
+                    if(i+1<argc) {
+                        info->Info = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagInfo++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("o") {
+                    if(i+1<argc) {
+                        info->Out = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagOut++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("c") {
+                    if(i+1<argc) {
+                        info->configFile = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagconfigFile++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("m") {
+                    if(i+1<argc) {
+                        info->mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagmode++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("h") {
+                    usage(argv[0]);
+                    exit(EXIT_SUCCESS);
+                    break;
+                }
+                SCASE("html") {
+                    htmlBeforeUsage(argv[0]);
+                    usage(argv[0]);
+                    htmlAfterUsage(argv[0]);
+                    exit(EXIT_SUCCESS);
+                    break;
+                }
+                SDEFAULT {
+                    fprintf(stderr, "Not Supported Options: :%s\n", argv[i]);
+                    usage(argv[0]);
+                    exit(EXIT_FAILURE);
+                    break;
+                }
+            SSWITCHEND;
+        } 
+    } 
+} 
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/init.c b/src/Tools/mrcImage/mrcImage3DPeakGet/src/init.c
new file mode 100755
index 0000000000..b7e9ea1bba
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/init.c
@@ -0,0 +1,91 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "../inc/config.h"
+#include "genUtil.h"
+#include "String.h"
+#include "File.h"
+#include "Memory.h"
+
+
+void
+init0(mrcImage3DPeakGetInfo* info)
+{
+    info->fptIn = NULL;    info->flagIn = 0;
+    info->fptInfo = stdin;    info->flagInfo = 0;
+    info->fptOut = stdout;    info->flagOut = 0;
+    info->fptconfigFile = NULL;    info->flagconfigFile = 0;
+    info->mode = 0;    info->flagmode = 0;
+}
+
+void
+init1(mrcImage3DPeakGetInfo* info)
+{
+    char s[1024];
+    int i;
+    if(!info->flagIn) {
+        stringGetFromFile(s, "In", stdin, stdout, 0);
+        info->In = stringGetNthWord(s, 1, " ,\t");
+        info->flagIn++;
+    }
+    if(info->flagIn) {
+        info->fptIn = fileOpen(info->In, "r");
+    }
+    
+    if(info->flagInfo) {
+        info->fptInfo = fileOpen(info->Info, "r");
+    }
+    
+    if(info->flagOut) {
+        info->fptOut = fileOpen(info->Out, "w");
+    }
+    
+    if(info->flagconfigFile) {
+        info->fptconfigFile = fileOpen(info->configFile, "r");
+    }
+    
+    if(info->flagmode) {
+    }
+    
+}
+#ifdef KHOROS
+#include <stdio.h>
+#include "bootstrap.h"
+#include "dataserv.h"
+#include "datamanip.h"
+extern void func_usage_additions(void);
+extern void func_free_args(kexit_status status, kaddr client_data);
+extern void func_get_args(kform* pane);
+
+void
+func_usage_additions(void)
+{
+}
+void
+func_free_args(kexit_status status, kaddr client_data)
+{
+}
+void
+func_get_args(kform* pane)
+{
+}
+void
+khorosInit(int argc, char* argv[])
+{
+    char* eospath;
+    char  panepath[1024];
+    FILE* fpt;
+    
+    eospath = getenv("EOS_HOME");
+    sprintf(panepath, "%s/src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.pane", eospath);
+    khoros_initialize(argc, argv, "EOS");
+    fpt = fopen(panepath, "r");    if(NULL!=fpt) {
+        fclose(fpt);
+        kclui_initialize(panepath, KGEN_NONE, "EOS", "mrcImage3DPeakGet",
+                     func_usage_additions,
+                     func_get_args,
+                     func_free_args);
+    }
+}
+#endif /* KHOROS */ 
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.c b/src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.c
new file mode 100755
index 0000000000..e2d3257719
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.c
@@ -0,0 +1,69 @@
+/*
+# mrcImage3DPeakGet : $Revision$  
+# $Date$ 
+# Created by $Author$
+# Usage : mrcImage3DPeakGet
+# Attention
+#   $Loccker$
+#  	$State$ 
+#
+*/
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>                  
+#define GLOBAL_DECLARATION
+#include "../inc/config.h"
+
+#define DEBUG
+#include "genUtil.h"
+#include "mrcImage.h"
+#include "lmrcImageROI2D.h"
+
+typedef struct lmrcImage3DPeakGetInfo {
+	lmrcImageROIsInfo     roiInfo;
+} lmrcImage3DPeakGetInfo;
+
+/*
+typedef enum lmrcImage3DPeakGetMode {
+	a=0,
+	b=1
+} lmrcImage3DPeakGetMode;
+*/
+
+int
+main(int argc, char* argv[]) 
+{
+	mrcImage3DPeakGetInfo info;
+	lmrcImage3DPeakGetInfo linfo;
+	mrcImage in;
+	mrcImage* out;
+	int i;
+	
+	init0(&info);
+    argCheck(&info, argc, argv);
+    init1(&info);
+
+	DEBUGPRINT("Program Start\n");
+	mrcFileRead(&in, info.In, "in main", 0);
+	lmrcImageROIsInformationGet(info.fptInfo, &linfo.roiInfo);
+
+	out = (mrcImage*)memoryAllocate(sizeof(mrcImage)*linfo.numROI, "in main (out)");
+
+	for(i=0; i<llinfo.numROI; i++) {
+	}
+
+	for(i=0; i<linfo.numROI; i++) {
+		mrcFileWrite(&(out[i]), linfo.ROI[i].FileName, "main", 0);
+	}
+	   
+	exit(EXIT_SUCCESS);
+}
+
+void
+additionalUsage()
+{
+	fprintf(stderr, "----- Additional Usage -----\n");
+}
+
+
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.pane b/src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.pane
new file mode 100755
index 0000000000..518fd59c95
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/mrcImage3DPeakGet.pane
@@ -0,0 +1,17 @@
+-F 4.3 1 0 52x1+0+0 +0+0 'Cantata' cantata
+  -M 1 1 52x1+0+0 +1+0 ' ' subform
+    -P 1 0 52x1+0+1 +0+0 ' ' mrcImage3DPeakGet
+      -D 1 0 9x1+0+0 'Options' _gui_options
+        -H 1  6x1+0+0 'License' 'license' $BOOTSTRAP/repos/license/License license
+        -E
+        -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrcImage3DPeakGet
+        -H 1  5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImage3DPeakGet/doc/mrcImage3DPeakGet.doc help
+        -Q 1 0 5.25x1+47+0 'Close'
+        -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input:3D' i
+        -I 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'Info' 'Input:ROI Info' I
+        -O 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'Out' 'Output:Positon' o
+        -I 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'configFile' 'ConfigurationFile' c
+        -i 1 0 1 0 0 -1x1+1+7.500000 0 0 0 0 0 'mode' 'Mode' m
+    -E
+  -E
+-E
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/usage.c b/src/Tools/mrcImage/mrcImage3DPeakGet/src/usage.c
new file mode 100755
index 0000000000..d183b3f4b6
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/usage.c
@@ -0,0 +1,37 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+
+void
+usage(char* thisProgram)
+{
+    fprintf(stderr, "Usage: %s\n", thisProgram);
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:3D\n");
+    fprintf(stderr, "    [-I[nformation]      Info                (stdin     ).as(inFile::ASCII       ) ] :Optional  :Input:ROI Info\n");
+    fprintf(stderr, "    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:Positon\n");
+    fprintf(stderr, "    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile\n");
+    fprintf(stderr, "    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode\n");
+    additionalUsage();
+}
+
+void
+htmlBeforeUsage(char* thisProgram)
+{
+    fprintf(stderr, "<HTML>\n");
+    fprintf(stderr, "<HEAD>\n");
+    fprintf(stderr, "<TITLE>%s</TITLE>\n", thisProgram);
+    fprintf(stderr, "</HEAD>\n");
+    fprintf(stderr, "<BODY>\n");
+    fprintf(stderr, "<H1>%s</H1>\n", thisProgram);
+    fprintf(stderr, "<H2>Usage</H2>\n");
+    fprintf(stderr, "<PRE>\n");
+}
+
+void
+htmlAfterUsage(char* thisProgram)
+{
+    fprintf(stderr, "</PRE>\n");
+    fprintf(stderr, "</BODY>\n");
+    fprintf(stderr, "</HTML>\n");
+}
diff --git a/src/Tools/mrcImage/mrcImage3DPeakGet/src/util.c b/src/Tools/mrcImage/mrcImage3DPeakGet/src/util.c
new file mode 100755
index 0000000000..ee5e5f2324
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImage3DPeakGet/src/util.c
@@ -0,0 +1,4 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+
diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/Config/OptionControlFile
index 6528034a82..39c54d26eb 100755
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/Config/OptionControlFile
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/Config/OptionControlFile
@@ -1,8 +1,9 @@
 # OptionControlFile
 # FileFormat
-"-i","-i[nput]","InputDataFile","Essential","1","1","In","inFile","NULL"
-"-o","-o[utput]","OutputDataFile","Essential","1","1","Out","outFile","NULL"
-"-O","-O[utput]","Output WindowedFile","Optional","1","1","OutWin","outFile","NULL"
+"-i","-i[nput]","Input","Essential","1","1","In","inFile::mrcImage","NULL"
+"-o","-o[utput]","Output","Essential","1","1","Out","outFile::mrcImage","NULL"
+"-oc","-o[utput]c[entre]","OutputDataFile","Optional","1","1","OutCentre","outFile::mrcImage","NULL"
+"-O","-O[utput]","Output WindowedFile","Optional","1","1","OutWin","outFile::mrcImage","NULL"
 "-Wy","-W[indowing]y","Window Height: N.y * 1/Wy","Optional","1","1","Wy","Real","6"
 "-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
 "-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/inc/mrcImageAutoCorrelationWithWindowing.h b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/inc/mrcImageAutoCorrelationWithWindowing.h
index a56b070d2c..8ca4b04ddc 100755
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/inc/mrcImageAutoCorrelationWithWindowing.h
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/inc/mrcImageAutoCorrelationWithWindowing.h
@@ -21,6 +21,10 @@ typedef struct mrcImageAutoCorrelationWithWindowingInfo {
     char* Out;
     FILE* fptOut;
     
+    long flagOutCentre;
+    char* OutCentre;
+    FILE* fptOutCentre;
+    
     long flagOutWin;
     char* OutWin;
     FILE* fptOutWin;
diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/argCheck.c b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/argCheck.c
index bc68bb1326..27c32acb7b 100755
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/argCheck.c
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/argCheck.c
@@ -50,6 +50,17 @@ argCheck(mrcImageAutoCorrelationWithWindowingInfo* info, int argc, char* argv[])
                     }
                     SBREAK;
                 }
+                SCASE("oc") {
+                    if(i+1<argc) {
+                        info->OutCentre = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagOutCentre++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
                 SCASE("O") {
                     if(i+1<argc) {
                         info->OutWin = stringGetNthWord(argv[i+1], 1, " ,");
diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/init.c b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/init.c
index 302b6b9ded..98381d8bd9 100755
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/init.c
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/init.c
@@ -14,6 +14,7 @@ init0(mrcImageAutoCorrelationWithWindowingInfo* info)
 {
     info->fptIn = NULL;    info->flagIn = 0;
     info->fptOut = NULL;    info->flagOut = 0;
+    info->fptOutCentre = NULL;    info->flagOutCentre = 0;
     info->fptOutWin = NULL;    info->flagOutWin = 0;
     info->Wy = 6;    info->flagWy = 0;
     info->fptconfigFile = NULL;    info->flagconfigFile = 0;
@@ -43,6 +44,10 @@ init1(mrcImageAutoCorrelationWithWindowingInfo* info)
         info->fptOut = fileOpen(info->Out, "w");
     }
     
+    if(info->flagOutCentre) {
+        info->fptOutCentre = fileOpen(info->OutCentre, "w");
+    }
+    
     if(info->flagOutWin) {
         info->fptOutWin = fileOpen(info->OutWin, "w");
     }
diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.pane b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.pane
index 5e032d0d92..8ef5309bad 100755
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.pane
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.pane
@@ -7,12 +7,13 @@
         -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrcImageAutoCorrelationWithWindowing
         -H 1  5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/doc/mrcImageAutoCorrelationWithWindowing.doc help
         -Q 1 0 5.25x1+47+0 'Close'
-        -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'InputDataFile' i
-        -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'OutputDataFile' o
-        -O 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'OutWin' 'Output WindowedFile' O
-        -f 1 0 1 0 0 -1x1+1+6.000000 0 0 6.000000 0 0 0 'Wy' 'Window Height: N.y * 1/Wy' Wy
-        -I 1 0 1 0 0 1 -1x1+1+7.500000 ' ' 'configFile' 'ConfigurationFile' c
-        -i 1 0 1 0 0 -1x1+1+9.000000 0 0 0 0 0 'mode' 'Mode' m
+        -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input' i
+        -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'Output' o
+        -O 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'OutCentre' 'OutputDataFile' oc
+        -O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'OutWin' 'Output WindowedFile' O
+        -f 1 0 1 0 0 -1x1+1+7.500000 0 0 6.000000 0 0 0 'Wy' 'Window Height: N.y * 1/Wy' Wy
+        -I 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'configFile' 'ConfigurationFile' c
+        -i 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'mode' 'Mode' m
     -E
   -E
 -E
diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/test/Makefile b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/test/Makefile
new file mode 100755
index 0000000000..20c14e56e2
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/test/Makefile
@@ -0,0 +1,23 @@
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+include ../../../../../Config/Define.inc
+
+all: help exec
+
+DATA=data/TEM_filter_sample
+
+help:
+	@echo "----- Help Message Check -----"
+	@../$(OSTYPE)/$(OBJECTNAME)	 -h
+
+exec:
+	@echo "----- Execution Check -----"
+	../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).open -o $(DATA).auto -O $(DATA).win -Wy 1
+	@echo "----- Calc check -----"		
+
+clean:
+
+init:
+	mrcImageBinalization -i $(DATA).mrc -o $(DATA).bin -t 240
+	mrcImageOpening -i $(DATA).bin -o $(DATA).open -times 2 -m 2 -r 1
diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/test/data b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/test/data
new file mode 120000
index 0000000000..fccad5f901
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/test/data
@@ -0,0 +1 @@
+../../../../../..//data/mrcImageAutoCorrelationWithWindowing
\ No newline at end of file
diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/usage.c b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/usage.c
index fcb17c84b6..2d1f769e36 100755
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/usage.c
@@ -7,9 +7,10 @@ usage(char* thisProgram)
 {
     fprintf(stderr, "Usage: %s\n", thisProgram);
     fprintf(stderr, "Options:\n");
-    fprintf(stderr, "    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile\n");
-    fprintf(stderr, "    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile\n");
-    fprintf(stderr, "    [-O[utput]           OutWin              (NULL      ).as(outFile             ) ] :Optional  :Output WindowedFile\n");
+    fprintf(stderr, "    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input\n");
+    fprintf(stderr, "    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output\n");
+    fprintf(stderr, "    [-o[utput]c[entre]   OutCentre           (NULL      ).as(outFile::mrcImage   ) ] :Optional  :OutputDataFile\n");
+    fprintf(stderr, "    [-O[utput]           OutWin              (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output WindowedFile\n");
     fprintf(stderr, "    [-W[indowing]y       Wy                  (6         ).as(Real                ) ] :Optional  :Window Height: N.y * 1/Wy\n");
     fprintf(stderr, "    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile\n");
     fprintf(stderr, "    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode\n");
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/Config/Define.inc b/src/Tools/mrcImage/mrcImageSNEstimate/Config/Define.inc
new file mode 100755
index 0000000000..892f89eff5
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/Config/Define.inc
@@ -0,0 +1,4 @@
+OBJECTNAME = mrcImageSNEstimate
+EXTRA_LIB  =
+EXTRA_CCOPTS =
+EXTRA_INC =
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageSNEstimate/Config/OptionControlFile
new file mode 100755
index 0000000000..465fc1c195
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/Config/OptionControlFile
@@ -0,0 +1,6 @@
+# OptionControlFile
+# FileFormat
+"-i","-i[nput]","InputDataFile","Essential","1","1","In","inFile","NULL"
+"-o","-o[utput]","OutputDataFile","Essential","1","1","Out","outFile","NULL"
+"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
+"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/Config/Target.inc b/src/Tools/mrcImage/mrcImageSNEstimate/Config/Target.inc
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/Makefile b/src/Tools/mrcImage/mrcImageSNEstimate/Makefile
new file mode 100755
index 0000000000..6c4a33690a
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/Makefile
@@ -0,0 +1,115 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+	cd src; make all; cd ..
+
+install:
+	cd src; make install; cd ..
+
+
+putSF:
+	if [ -f private ] ; \
+	then \
+		echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+	else \
+		cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+	fi
+
+put:
+	cd src; make put; cd ..
+
+clean:
+	cd src; make clean; cd ..
+
+depend:
+	cd src; make depend; cd ..
+
+check:
+	@if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+		echo making directory; \
+		mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+	fi
+	ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+	@$(RM) src/Makefile
+	@echo "New src/Makefile" 
+	@$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+	@cd src; touch $(OSTYPE)/.Depend; make depend
+
+update:
+	@if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+		echo making directory; \
+		mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+	fi
+	ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+	@$(RM) src/Makefile
+	@echo "New src/Makefile" 
+	@$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+	@cd src; touch $(OSTYPE)/.Depend; echo "Y" | make update      
+
+cvsupdate::
+	cvs -d $(EOS_CVSROOT) update -d 
+
+cvscommit::
+	cvs -d $(EOS_CVSROOT) commit
+
+backup:
+	@cd ../../../..;     \
+	echo $(OBJECTNAME) ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config	; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+	tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+	@cd ../../../..;     \
+	echo $(OBJECTNAME) ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config	; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+	tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+	
+distribute:
+	cd ../../../..;     \
+	echo $(OBJECTNAME) ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config	; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+	tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+	
+distribute-all:
+	@cd ../../../..;     \
+	echo $(OBJECTNAME) ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config	; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+	tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+	${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
+
+include Config/Target.inc
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/doc/Makefile b/src/Tools/mrcImage/mrcImageSNEstimate/doc/Makefile
new file mode 100755
index 0000000000..8215199e1b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/doc/Makefile
@@ -0,0 +1,2 @@
+install:
+	cd ../src; make install-doc; cd ../doc	
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/inc/config.h b/src/Tools/mrcImage/mrcImageSNEstimate/inc/config.h
new file mode 100755
index 0000000000..5c7718b7b3
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/inc/config.h
@@ -0,0 +1,6 @@
+#ifndef CONFIG_H
+#define CONFIG_H
+
+#include "../inc/mrcImageSNEstimate.h"
+
+#endif /* CONFIG_H */
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/inc/mrcImageSNEstimate.h b/src/Tools/mrcImage/mrcImageSNEstimate/inc/mrcImageSNEstimate.h
new file mode 100755
index 0000000000..bcdbd442f4
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/inc/mrcImageSNEstimate.h
@@ -0,0 +1,46 @@
+#ifndef MRCIMAGESNESTIMATE_H
+#define MRCIMAGESNESTIMATE_H
+#include <stdio.h>
+#include <stdlib.h>
+
+#define OPTION_FLAG     '-'
+#define OPTION_FLAG_POS (0)
+#define OPTION_POS      (1)
+
+
+
+
+typedef struct mrcImageSNEstimateInfo {
+    long flagRedirect;
+
+    long flagIn;
+    char* In;
+    FILE* fptIn;
+    
+    long flagOut;
+    char* Out;
+    FILE* fptOut;
+    
+    long flagconfigFile;
+    char* configFile;
+    FILE* fptconfigFile;
+    
+    long flagmode;
+    long mode;
+    
+} mrcImageSNEstimateInfo;
+#ifdef __cplusplus
+extern "C" {
+#endif
+extern void argCheck(mrcImageSNEstimateInfo* info, int argc, char* avgv[]);
+extern void khorosInit(int argc, char* avgv[]);
+extern void init0(mrcImageSNEstimateInfo* info);
+extern void init1(mrcImageSNEstimateInfo* info);
+extern void usage(char* usage);
+extern void additionalUsage(void);
+extern void htmlBeforeUsage(char* usage);
+extern void htmlAfterUsage(char* usage);
+#ifdef __cplusplus
+};
+#endif
+#endif /* MRCIMAGESNESTIMATE_H */
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/.Depend b/src/Tools/mrcImage/mrcImageSNEstimate/src/.Depend
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/.Source b/src/Tools/mrcImage/mrcImageSNEstimate/src/.Source
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/Makefile b/src/Tools/mrcImage/mrcImageSNEstimate/src/Makefile
new file mode 100755
index 0000000000..7beb110976
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/Makefile
@@ -0,0 +1,427 @@
+include ../Config/Define.inc
+include ../../Config/Define.inc
+include ../../../Config/Define.inc
+include ../../../../Config/Define.inc
+
+EOSHOME=../../../../../
+DSTDIR=$(EOSHOME)/bin
+DSTDOC=$(EOSHOME)/doc
+DSTTAR=$(EOSHOME)/tar
+
+INCFILES   = 
+
+LIBFILES   = \
+			$(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+			$(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+			$(OBJECTNAME).c \
+			init.c \
+			argCheck.c \
+			usage.c  \
+			util.c \
+
+SRCCXX  = \
+			$(OBJECTNAME).cc \
+			init.cc \
+			argCheck.cc \
+			usage.cc  \
+			util.cc \
+
+MODULES    = \
+			$(OBJECTNAME).o \
+			init.o \
+			argCheck.o \
+			usage.o  \
+			util.o \
+
+REALMODULES    = \
+			$(OSTYPE)/$(OBJECTNAME).o \
+			$(OSTYPE)/init.o \
+			$(OSTYPE)/argCheck.o \
+			$(OSTYPE)/usage.o \
+			$(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+			$(OBJECTNAME).debugo \
+			init.debugo \
+			argCheck.debugo \
+			usage.debugo  \
+			util.debugo \
+
+REALMODULESDEBUG    = \
+			$(OSTYPE)/$(OBJECTNAME).debugo \
+			$(OSTYPE)/init.debugo \
+			$(OSTYPE)/argCheck.debugo \
+			$(OSTYPE)/usage.debugo \
+			$(OSTYPE)/util.debugo 
+
+
+all: $(OSTYPE)/$(OBJECTNAME) 
+	if [ ! -L $(OSTYPE) ] ; then \
+		moveHostdependent; \
+	fi
+
+debug: $(OSTYPE)/$(OBJECTNAME).debug
+
+cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb
+
+
+$(OSTYPE)/$(OBJECTNAME)::
+	@$(RM) -f $(OSTYPE)/Makefile ; \
+	$(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+	cd $(OSTYPE); \
+	$(MAKE) $(OBJECTNAME)  WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+$(OSTYPE)/$(OBJECTNAME).debug::
+	@$(RM) -f $(OSTYPE)/Makefile ; \
+	$(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+	cd $(OSTYPE); \
+	$(MAKE) $(OBJECTNAME).debug  WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+$(OSTYPE)/$(OBJECTNAME).cudagdb::
+	@$(RM) -f $(OSTYPE)/Makefile ; \
+	$(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
+	cd $(OSTYPE); \
+	$(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
+
+cvsupdate::
+	cvs -d $(EOS_CVSROOT) update -d	
+
+cvscommit::
+	cvs -d $(EOS_CVSROOT) commit 
+
+edit:
+	@if [ -r $(OBJECTNAME).c ]; \
+	then \
+		sccsEdit $(OBJECTNAME).c; \
+	else \
+		echo "Source files are already editable"; \
+	fi
+	@if [ -r wish/$(OBJECTNAME).wish ]; \
+	then \
+		cd wish; sccsEdit $(OBJECTNAME).wish; \
+	else \
+		echo "Source files (wish) are already editable."; \
+	fi
+	@if [ -r ruby/$(OBJECTNAME).rb ]; \
+	then \
+		cd ruby; sccsEdit $(OBJECTNAME).rb; \
+	else \
+		echo "Source files (ruby) are already editable."; \
+	fi
+	@if [ -r perl/$(OBJECTNAME).pl ]; \
+	then \
+		cd perl; sccsEdit $(OBJECTNAME).pl ; \
+	else \
+		echo "Source files (perl) are already editable."; \
+	fi
+	@if [ -r ../Config/OptionControlFile ]; \
+	then \
+		cd ../Config; sccsEdit OptionControlFile; \
+	else \
+		echo "OptionControlFile are already editable."; \
+	fi
+	
+unedit:
+	@if [ -w $(OBJECTNAME).c ]; \
+	then \
+		sccsUnedit $(OBJECTNAME).c; \
+	else \
+		echo "Source files are not editable"; \
+	fi
+	@if [ -w wish/$(OBJECTNAME).wish ]; \
+	then \
+		cd wish; sccsUnedit $(OBJECTNAME).wish; \
+	else \
+		echo "Source files (wish) are not editable."; \
+	fi
+	@if [ -w ruby/$(OBJECTNAME).rb]; \
+	then \
+		cd ruby; sccsUnedit $(OBJECTNAME).rb; \
+	else \
+		echo "Source files (ruby) are not editable."; \
+	fi
+	@if [ -w perl/$(OBJECTNAME).pl ]; \
+	then \
+		cd perl; sccsUnedit $(OBJECTNAME).pl ; \
+	else \
+		echo "Source files (ruby) are not editable."; \
+	fi
+	@if [ -w ../Config/OptionControlFile ]; \
+	then \
+		cd ../Config; sccsUnedit OptionControlFile; \
+	else \
+		echo "OptionControlFile are not editable."; \
+	fi
+	
+report:
+	@if [ -r $(OBJECTNAME).c ]; \
+	then \
+		sccsReport $(OBJECTNAME).c; \
+	else \
+		echo "Source files are already editable"; \
+	fi
+	@if [ -r wish/$(OBJECTNAME).wish ]; \
+	then \
+		cd wish; sccsReport $(OBJECTNAME).wish; \
+	else \
+		echo "Source files (wish) are already editable."; \
+	fi
+	@if [ -r ruby/$(OBJECTNAME).rb ]; \
+	then \
+		cd ruby; sccsReport $(OBJECTNAME).rb; \
+	else \
+		echo "Source files (ruby) are already editable."; \
+	fi
+	@if [ -r perl/$(OBJECTNAME).pl ] ; \
+	then \
+		cd perl; sccsReport $(OBJECTNAME).pl ; \
+	else \
+		echo "Source files (perl) are already editable."; \
+	fi
+	@if [ -r ../Config/OptionControlFile ]; \
+	then \
+		cd ../Config; sccsReport OptionControlFile; \
+	else \
+		echo "OptionControlFile are already editable."; \
+	fi
+
+clean : 
+	rm -f *.debugo $(OSTYPE)/*.debugo *.cudagdbo $(OSTYPE)/*.cudagdbo *.o $(OSTYPE)/*.o *.linkinfo $(OSTYPE)/*.linkinfo \
+		$(OSTYPE)/$(OBJECTNAME) $(OSTYPE)/*.$(OSTYPE) \
+		$(OSTYPE)/$(OBJECTNAME).debug $(OSTYPE)/*.$(OSTYPE).debug \
+		$(OSTYPE)/$(OBJECTNAME).cudagdb $(OSTYPE)/*.$(OSTYPE).cudagdb \
+		$(OSTYPE)/$(OBJECTNAME).linkinfo $(OSTYPE)/*.$(OSTYPE).linkinfo \
+		*.bak *.$(OSTYPE) core
+
+install: install-bin install-doc install-wish install-ruby install-shell install-perl
+	@if [ dummy$(KHOROS_KENGOBJ) != dummy ]  ; \
+	then \
+		if [ -x $(KHOROS_KGENOBJ) ] ;  \
+		then \
+			make install-khoros ; \
+		fi; \
+	fi 
+
+install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) 
+
+$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME) 
+	@echo ---- Installing to bin
+	@echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
+	@if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \
+	then \
+		mkdir $(DSTDIR)/$(OSTYPE); \
+	fi
+	@if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
+	then \
+		echo "Compilation is complete"; \
+		$(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+		$(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
+		$(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
+	else \
+		echo "Compilation is incomplete. $(OBJECTNAME)"; \
+	fi
+	@echo ---- end of bin
+
+install-wish:
+	@if [ -d wish ]; \
+	then \
+		echo "---- Tcl/Tk file Install"; \
+		if [ ! -d $(DSTDIR)/wish/$(OBJECTNAME) ]; \
+		then \
+			mkdir $(DSTDIR)/wish/$(OBJECTNAME) ; \
+		fi ; \
+		$(CP) -f wish/* $(DSTDIR)/wish/$(OBJECTNAME); \
+		$(CHMOD) 555 $(DSTDIR)/wish/$(OBJECTNAME)/*  ;\
+		touch $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
+		$(CHMOD) 666 $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
+		echo "---- Tcl/Tk file Installed";\
+	fi
+
+install-ruby:
+	@if [ -d ruby ]; \
+	then \
+		echo "---- Ruby/Tk file Install"; \
+		if [ ! -d $(DSTDIR)/ruby/$(OBJECTNAME) ]; \
+		then \
+			mkdir $(DSTDIR)/ruby/$(OBJECTNAME) ; \
+		fi ; \
+		$(CP) -f ruby/* $(DSTDIR)/ruby/$(OBJECTNAME); \
+		$(CHMOD) 555 $(DSTDIR)/ruby/$(OBJECTNAME)/* ; \
+		echo "---- Ruby/Tk file Installed"; \
+	fi
+
+install-perl:
+	@if [ -d perl ]; \
+	then \
+		echo "---- Perl/Tk file Install"; \
+		if [ ! -d $(DSTDIR)/perl/$(OBJECTNAME) ]; \
+		then \
+			mkdir $(DSTDIR)/perl/$(OBJECTNAME) ; \
+		fi; \
+		$(CP) -f perl/* $(DSTDIR)/perl/$(OBJECTNAME); \
+		$(CHMOD) 555 $(DSTDIR)/perl/$(OBJECTNAME)/* ; \
+		echo "---- Perl/Tk file Installed"; \
+	fi
+
+install-shell:
+	@if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
+	then \
+		mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
+	fi
+	@if [ -d shell ]; \
+	then \
+		echo "---- Shell file Install"; \
+		if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
+		then \
+			mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
+		fi ; \
+		$(CP) -f shell/* $(DSTDIR)/shell/$(OBJECTNAME); \
+		$(CHMOD) 555 $(DSTDIR)/shell/$(OBJECTNAME)/*; \
+		echo "---- Shell file Installed"; \
+	fi
+
+install-khoros:
+	@echo Installing to khoros
+	@if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KGENOBJ) ]; \
+	then \
+		echo kgenobj;\
+		$(KHOROS_KGENOBJ) -tb Eos -oname $(OBJECTNAME) -type script -pane -cantata true -cat Eos -subcat $(CLASSNAME) -description $(OBJECTNAME) -bname $(OBJECTNAME) -form  -lang ksh ; \
+	fi
+	@if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
+	then \
+		$(KHOROS_KSET) -tb Eos -oname $(OBJECTNAME) -icon $(OBJECTNAME) ; \
+	fi
+	@if [ -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
+	then \
+		$(CHMOD) -R 775 ../../../../../objects/script/$(OBJECTNAME) ; \
+		if [ $?  ] ; \
+		then \
+			echo "-- setting khoros ---" ; \
+			if [ -d ../../../../../objects/script/$(OBJECTNAME)/uis/ ] ; \
+			then \
+				$(CD) ../../../../../objects/script/$(OBJECTNAME)/uis/ ; \
+				$(RM) -f $(OBJECTNAME).pane ; \
+				$(LN) -s ../../../../src/Tools/$(CLASSNAME)/$(OBJECTNAME)/src/$(OBJECTNAME).pane $(OBJECTNAME).pane; \
+				$(CD) ../../ ; \
+				$(CHMOD) -R 555 $(OBJECTNAME); \
+			else \
+				echo "../../../../../objects/script/$(OBJECTNAME)/uis/ does not exist."; \
+			fi ; \
+		else \
+			echo "Failed !!: Cannot chage mode in installing  $(OBJECTNAME) to khoros system"; \
+		fi ; \
+		echo "-- end of khoros-installing"; \
+	fi
+
+install-doc: html 
+	@if [ ! -d $(DSTDOC)/SmallTools ]; \
+	then \
+		mkdir $(DSTDOC)/SmallTools ;\
+	fi
+	@if [ -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ]; \
+	then \
+		$(RM) -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ;\
+	fi
+	@$(CP) $(OBJECTNAME).html  $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+	@$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+	@if [ -f ../doc/*.html ]; \
+	then \
+		$(CP) ../doc/*.html  $(DSTDOC)/SmallTools/ ;\
+	fi
+	@$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
+	@if [ -f $(DSTDOC)/SmallTools/Makefile ]; \
+	then \
+		cd $(DSTDOC)/SmallTools; $(MAKE); \
+	fi
+
+html: $(OBJECTNAME).html
+
+configFileRead:
+	@ctrl2configFileRead $(CLASSNAME) $(OBJECTNAME) ../Config/OptionControlFile
+
+$(OBJECTNAME).html: $(OSTYPE)/$(OBJECTNAME)
+	@echo creating html
+	@$(OSTYPE)/$(OBJECTNAME) -html 2> $(OBJECTNAME).html.tmp
+	@sed -e s/$(OSTYPE)\\/// $(OBJECTNAME).html.tmp > $(OBJECTNAME).html
+	@$(RM) $(OBJECTNAME).html.tmp
+
+$(DSTDIR)/$(OBJECTNAME): $(OSTYPE)/$(OBJECTNAME)
+	@ln -s -f ../sbin/MachineIndependent $@
+
+depend::
+	@echo dependency checking now
+	@if [ ! -L $(OSTYPE) ] ; then \
+		moveHostdependent; \
+	fi
+	rm -f $(OSTYPE)/.Depend	
+	#echo C
+	@if [ -f $(OBJECTNAME).c ] ; \
+	then \
+		echo "dependency: *.c"; \
+		echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c   ; \
+		     $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c                  >> $(OSTYPE)/.Depend ; \
+	fi
+	#echo CC
+	@if [ -f $(OBJECTNAME).cc ] ; \
+	then \
+		echo "dependency: *.cc"; \
+		echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc ; \
+		     $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc >> $(OSTYPE)/.Depend ; \
+	fi
+	@if [ -f $(OBJECTNAME).ccm ] ; \
+	then \
+		echo "dependency: *.ccm"; \
+		echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm ; \
+		     $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm >> $(OSTYPE)/.Depend ; \
+	fi
+	@if [ -f $(OBJECTNAME).cu ] ; \
+	then \
+		echo "dependency: *.cu"; \
+		echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu ; \
+		     $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu >> $(OSTYPE)/.Depend ; \
+	fi
+
+update:../Config/OptionControlFile
+	maketool $(CLASSNAME) $(OBJECTNAME) update
+
+changeName::
+
+Test:$(OSTYPE)/$(OBJECTNAME) TestDir
+	@if [ -f test/Makefile ] ; \
+	then \
+		cd test; make ; \
+	else \
+		echo "No test Makefile"; \
+	fi
+
+TestDir::
+	@if [ ! -d test ] ; \
+	then \
+		echo "Creating test dir"; \
+		mkdir  test; \
+	fi
+	@if [ ! -f test/Makefile ] ; \
+	then \
+		echo "Creating Makefile"; \
+		cd test; \
+		protoTestMakefileCreate; \
+	fi
+	@if [ ! -d test/data ]; \
+	then \
+		mkdir $(EOSHOME)/data/$(OBJECTNAME); \
+		cd test; \
+		ln -sf ../$(EOSHOME)/data/$(OBJECTNAME) data; \
+	fi 
+
+tar::
+	cd $(DSTTAR); tar cvf Tools.$(CLASSNAME).$(OBJECTNAME).tar ../bin/$(OBJECTNAME) \
+	                                                     ../bin/*/$(OBJECTNAME).* \
+	                                                     ../src/Tools/$(CLASSNAME)/$(OBJECTNAME) \
+				; gzip Tools.$(CLASSNAME).$(OBJECTNAME).tar
+
+-include $(OSTYPE)/.Depend
+-include ../Config/Target.inc
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/X86MAC64 b/src/Tools/mrcImage/mrcImageSNEstimate/src/X86MAC64
new file mode 120000
index 0000000000..ae7f607b43
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/X86MAC64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageSNEstimate/src/X86MAC64
\ No newline at end of file
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/argCheck.c b/src/Tools/mrcImage/mrcImageSNEstimate/src/argCheck.c
new file mode 100755
index 0000000000..b752d42600
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/argCheck.c
@@ -0,0 +1,96 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "../inc/config.h"
+#include "genUtil.h"
+#include "String.h"
+#include "File.h"
+#include "Memory.h"
+
+
+void
+argCheck(mrcImageSNEstimateInfo* info, int argc, char* argv[])
+{
+    long i;
+    char s[1024];
+    FILE* fpt;
+    
+    if(NULL==(fpt=fopen(".EosLog", "a+"))) { 
+        
+    } else {
+        for(i=0; i<argc; i++) {
+            fprintf(fpt, "%s ", argv[i]);
+        }
+        fprintf(fpt, "\n");
+        fclose(fpt);
+    }
+    for(i=1; i<argc; i++) {
+        if(OPTION_FLAG==argv[i][OPTION_FLAG_POS]) {
+            SSWITCH(argv[i]+OPTION_POS)
+                SCASE("i") {
+                    if(i+1<argc) {
+                        info->In = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagIn++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("o") {
+                    if(i+1<argc) {
+                        info->Out = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagOut++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("c") {
+                    if(i+1<argc) {
+                        info->configFile = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagconfigFile++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("m") {
+                    if(i+1<argc) {
+                        info->mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagmode++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
+                SCASE("h") {
+                    usage(argv[0]);
+                    exit(EXIT_SUCCESS);
+                    break;
+                }
+                SCASE("html") {
+                    htmlBeforeUsage(argv[0]);
+                    usage(argv[0]);
+                    htmlAfterUsage(argv[0]);
+                    exit(EXIT_SUCCESS);
+                    break;
+                }
+                SDEFAULT {
+                    fprintf(stderr, "Not Supported Options: :%s\n", argv[i]);
+                    usage(argv[0]);
+                    exit(EXIT_FAILURE);
+                    break;
+                }
+            SSWITCHEND;
+        } 
+    } 
+} 
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/init.c b/src/Tools/mrcImage/mrcImageSNEstimate/src/init.c
new file mode 100755
index 0000000000..85f20aaeb8
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/init.c
@@ -0,0 +1,91 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "../inc/config.h"
+#include "genUtil.h"
+#include "String.h"
+#include "File.h"
+#include "Memory.h"
+
+
+void
+init0(mrcImageSNEstimateInfo* info)
+{
+    info->fptIn = NULL;    info->flagIn = 0;
+    info->fptOut = NULL;    info->flagOut = 0;
+    info->fptconfigFile = NULL;    info->flagconfigFile = 0;
+    info->mode = 0;    info->flagmode = 0;
+}
+
+void
+init1(mrcImageSNEstimateInfo* info)
+{
+    char s[1024];
+    int i;
+    if(!info->flagIn) {
+        stringGetFromFile(s, "In", stdin, stdout, 0);
+        info->In = stringGetNthWord(s, 1, " ,\t");
+        info->flagIn++;
+    }
+    if(info->flagIn) {
+        info->fptIn = fileOpen(info->In, "r");
+    }
+    
+    if(!info->flagOut) {
+        stringGetFromFile(s, "Out", stdin, stdout, 0);
+        info->Out = stringGetNthWord(s, 1, " ,\t");
+        info->flagOut++;
+    }
+    if(info->flagOut) {
+        info->fptOut = fileOpen(info->Out, "w");
+    }
+    
+    if(info->flagconfigFile) {
+        info->fptconfigFile = fileOpen(info->configFile, "r");
+    }
+    
+    if(info->flagmode) {
+    }
+    
+}
+#ifdef KHOROS
+#include <stdio.h>
+#include "bootstrap.h"
+#include "dataserv.h"
+#include "datamanip.h"
+extern void func_usage_additions(void);
+extern void func_free_args(kexit_status status, kaddr client_data);
+extern void func_get_args(kform* pane);
+
+void
+func_usage_additions(void)
+{
+}
+void
+func_free_args(kexit_status status, kaddr client_data)
+{
+}
+void
+func_get_args(kform* pane)
+{
+}
+void
+khorosInit(int argc, char* argv[])
+{
+    char* eospath;
+    char  panepath[1024];
+    FILE* fpt;
+    
+    eospath = getenv("EOS_HOME");
+    sprintf(panepath, "%s/src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.pane", eospath);
+    khoros_initialize(argc, argv, "EOS");
+    fpt = fopen(panepath, "r");    if(NULL!=fpt) {
+        fclose(fpt);
+        kclui_initialize(panepath, KGEN_NONE, "EOS", "mrcImageSNEstimate",
+                     func_usage_additions,
+                     func_get_args,
+                     func_free_args);
+    }
+}
+#endif /* KHOROS */ 
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.c b/src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.c
new file mode 100755
index 0000000000..e3544b6101
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.c
@@ -0,0 +1,53 @@
+/*
+# mrcImageSNEstimate : $Revision$  
+# $Date$ 
+# Created by $Author$
+# Usage : mrcImageSNEstimate
+# Attention
+#   $Loccker$
+#  	$State$ 
+#
+*/
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>                  
+#define GLOBAL_DECLARATION
+#include "../inc/config.h"
+
+#define DEBUG
+#include "genUtil.h"
+#include "Class.h"
+
+/*
+Example:
+typedef struct lmrcImageSNEstimateInfo {
+	float a;
+	int   b;
+} lmrcImageSNEstimateInfo;
+
+typedef enum lmrcImageSNEstimateMode {
+	a=0,
+	b=1
+} lmrcImageSNEstimateMode;
+*/
+
+int
+main(int argc, char* argv[]) 
+{
+	mrcImageSNEstimateInfo info;
+
+	init0(&info);
+    argCheck(&info, argc, argv);
+    init1(&info);
+
+	DEBUGPRINT("Program Start\n");
+
+	exit(EXIT_SUCCESS);
+}
+
+void
+additionalUsage()
+{
+	fprintf(stderr, "----- Additional Usage -----\n");
+}
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.pane b/src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.pane
new file mode 100755
index 0000000000..854ed6cc62
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/mrcImageSNEstimate.pane
@@ -0,0 +1,16 @@
+-F 4.3 1 0 52x1+0+0 +0+0 'Cantata' cantata
+  -M 1 1 52x1+0+0 +1+0 ' ' subform
+    -P 1 0 52x1+0+1 +0+0 ' ' mrcImageSNEstimate
+      -D 1 0 9x1+0+0 'Options' _gui_options
+        -H 1  6x1+0+0 'License' 'license' $BOOTSTRAP/repos/license/License license
+        -E
+        -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrcImageSNEstimate
+        -H 1  5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImageSNEstimate/doc/mrcImageSNEstimate.doc help
+        -Q 1 0 5.25x1+47+0 'Close'
+        -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'InputDataFile' i
+        -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'OutputDataFile' o
+        -I 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'configFile' 'ConfigurationFile' c
+        -i 1 0 1 0 0 -1x1+1+6.000000 0 0 0 0 0 'mode' 'Mode' m
+    -E
+  -E
+-E
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/usage.c b/src/Tools/mrcImage/mrcImageSNEstimate/src/usage.c
new file mode 100755
index 0000000000..c3e4fc6eae
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/usage.c
@@ -0,0 +1,36 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+
+void
+usage(char* thisProgram)
+{
+    fprintf(stderr, "Usage: %s\n", thisProgram);
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile\n");
+    fprintf(stderr, "    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile\n");
+    fprintf(stderr, "    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile\n");
+    fprintf(stderr, "    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode\n");
+    additionalUsage();
+}
+
+void
+htmlBeforeUsage(char* thisProgram)
+{
+    fprintf(stderr, "<HTML>\n");
+    fprintf(stderr, "<HEAD>\n");
+    fprintf(stderr, "<TITLE>%s</TITLE>\n", thisProgram);
+    fprintf(stderr, "</HEAD>\n");
+    fprintf(stderr, "<BODY>\n");
+    fprintf(stderr, "<H1>%s</H1>\n", thisProgram);
+    fprintf(stderr, "<H2>Usage</H2>\n");
+    fprintf(stderr, "<PRE>\n");
+}
+
+void
+htmlAfterUsage(char* thisProgram)
+{
+    fprintf(stderr, "</PRE>\n");
+    fprintf(stderr, "</BODY>\n");
+    fprintf(stderr, "</HTML>\n");
+}
diff --git a/src/Tools/mrcImage/mrcImageSNEstimate/src/util.c b/src/Tools/mrcImage/mrcImageSNEstimate/src/util.c
new file mode 100755
index 0000000000..ee5e5f2324
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageSNEstimate/src/util.c
@@ -0,0 +1,4 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include "../inc/config.h"
+
diff --git a/src/Tools/mrcImage/mrcImageShapeSearch/src/mrcImageShapeSearch.c b/src/Tools/mrcImage/mrcImageShapeSearch/src/mrcImageShapeSearch.c
index 890eff2045..9011f3977b 100755
--- a/src/Tools/mrcImage/mrcImageShapeSearch/src/mrcImageShapeSearch.c
+++ b/src/Tools/mrcImage/mrcImageShapeSearch/src/mrcImageShapeSearch.c
@@ -75,7 +75,7 @@ extern void	lmrcImageShapeSearch(mrcImage* out, mrcImage* in, lmrcImageShapeSear
 extern void	lmrcImageShapeSearchCalc0(mrcImage* out, mrcImage* in, lmrcImageShapeSearchInfo* linfo, int mode);
 extern void	lmrcImageShapeSearchSylinder(double* data, mrcImage* in, Matrix3D mat, lmrcImageShapeSearchInfo* linfo, int mode);
 extern void	lmrcImageShapeSearchDisk(double* data, mrcImage* in, Matrix3D mat, lmrcImageShapeSearchInfo* linfo, int mode);
-extern void	lmrcImageShapeSearchSphere(double* data, mrcImage* in, lmrcImageShapeSearchInfo* linfo, int mode);
+extern void	lmrcImageShapeSearchSphere(double* data, mrcImage* in, Matrix3D mat, lmrcImageShapeSearchInfo* linfo, int mode);
 extern void lmrcImageShapeSearchModePrint(FILE* fpt);
 
 int
@@ -205,7 +205,7 @@ lmrcImageShapeSearchCalc0(mrcImage* out, mrcImage* in, lmrcImageShapeSearchInfo*
 	Array U;
 	Array C;
 	Array Lambda;
-	double L0, L1, L2;
+	double L0, L1, L2, L;
 	Array X;
 	Array Ave;
 	mrcImageParaTypeInteger nCube; 
@@ -269,11 +269,11 @@ lmrcImageShapeSearchCalc0(mrcImage* out, mrcImage* in, lmrcImageShapeSearchInfo*
 		for(srcz=-nCube/2; srcz<nCube/2; srcz++) {
 		for(srcy=-nCube/2; srcy<nCube/2; srcy++) {
 		for(srcx=-nCube/2; srcx<nCube/2; srcx++) {
-			//mrcPixelDataGet(in, x+srcx, y+srcy, z+srcz, &d, mrcPixelRePart, mrcPixelHowNearest);	
-			srcx0 = x + srcx;
-			srcy0 = y + srcy;
-			srcz0 = z + srcz;
-			k = srcx0 + srcy0*in->HeaderN.x + srcz0*in->HeaderN.x*in->HeaderN.y;
+			mrcPixelDataGet(in, x+srcx, y+srcy, z+srcz, &d, mrcPixelRePart, mrcPixelHowNearest);	
+			//srcx0 = x + srcx;
+			//srcy0 = y + srcy;
+			//srcz0 = z + srcz;
+			//k = srcx0 + srcy0*in->HeaderN.x + srcz0*in->HeaderN.x*in->HeaderN.y;
 			d = in->ImageFloatImage[k];
 			if(0<d) {
 				arrayDataSet2(X, 0, numPoint, srcx0);
@@ -293,9 +293,15 @@ lmrcImageShapeSearchCalc0(mrcImage* out, mrcImage* in, lmrcImageShapeSearchInfo*
 			L1 = arrayDataGet1(Lambda, 1);
 			L2 = arrayDataGet1(Lambda, 2);
 
+			L = L0+L1+L2;
+			L0 /= L;
+			L1 /= L;
+			L2 /= L;
+			
 			switch(mode) {
 				case lmrcImageShapeSearchModeSylinder: {	
-					W = ((L1!=0)?(L0/L1):1)*(L2!=0?(L0/L2):1);		
+					//W = ((L1!=0)?(L0/L1):1)*(L2!=0?(L0/L2):1);		
+					W = 1.0/(SQR(1-L0)+SQR(L1)+SQR(L2)); 
 #ifdef DEBUG
 					if(4000<W) {
 						DEBUGPRINT3("%f %f %f\n", x, y, z);
@@ -679,9 +685,8 @@ lmrcImageShapeSearchSphere(double* data, mrcImage* in, Matrix3D mat, lmrcImageSh
 		scoreNeg += d;
 		countNeg++;
 	}
-
-	}
 	}
+	
 	k0 =  (int)(linfo->x+0.5) + (int)(linfo->y+0.5)*in->HeaderN.x + (int)(linfo->z+0.5)*in->HeaderN.x*in->HeaderN.y; 
 	*data = (0.8*scorePos/countPos - 0.2*scoreNeg/countNeg);
 }
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/Config/OptionControlFile b/src/Tools/pdbUtil/pdb2mrc2d/Config/OptionControlFile
index a3edba5196..8c9e6a3ec1 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/Config/OptionControlFile
+++ b/src/Tools/pdbUtil/pdb2mrc2d/Config/OptionControlFile
@@ -15,4 +15,5 @@
 "-w","-w[eight]","weight","Optional","1","1","Weight","Real","1.0"
 "-sig","-sig[ma]","Sigma[A]:Atom radius","Optional","1","1","Sigma","Real","0.0"
 "-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
+"-cuda","-cuda","UseCuda","Optional","1","1","cudaDeviceID","Integer","0"
 "-m","-m[ode]","Mode: 0 Merc; 1: Earth","Optional","1","1","mode","Integer","0"
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/inc/pdb2mrc2d.h b/src/Tools/pdbUtil/pdb2mrc2d/inc/pdb2mrc2d.h
index c7e03e41aa..f279817464 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/inc/pdb2mrc2d.h
+++ b/src/Tools/pdbUtil/pdb2mrc2d/inc/pdb2mrc2d.h
@@ -101,6 +101,9 @@ typedef struct pdb2mrc2dInfo {
     char* configFile;
     FILE* fptconfigFile;
     
+    long flagcudaDeviceID;
+    long cudaDeviceID;
+    
     long flagmode;
     long mode;
     
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/argCheck.c b/src/Tools/pdbUtil/pdb2mrc2d/src/argCheck.c
index 447a2d6da7..93557fdc4e 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/argCheck.c
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/argCheck.c
@@ -232,6 +232,17 @@ argCheck(pdb2mrc2dInfo* info, int argc, char* argv[])
                     }
                     SBREAK;
                 }
+                SCASE("cuda") {
+                    if(i+1<argc) {
+                        info->cudaDeviceID = stringGetNthIntegerData(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagcudaDeviceID++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
                 SCASE("m") {
                     if(i+1<argc) {
                         info->mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/init.c b/src/Tools/pdbUtil/pdb2mrc2d/src/init.c
index 7560d79a67..0676b478c2 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/init.c
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/init.c
@@ -40,6 +40,7 @@ init0(pdb2mrc2dInfo* info)
     info->Weight = 1.0;    info->flagWeight = 0;
     info->Sigma = 0.0;    info->flagSigma = 0;
     info->fptconfigFile = NULL;    info->flagconfigFile = 0;
+    info->cudaDeviceID = 0;    info->flagcudaDeviceID = 0;
     info->mode = 0;    info->flagmode = 0;
 }
 
@@ -161,6 +162,9 @@ init1(pdb2mrc2dInfo* info)
         info->fptconfigFile = fileOpen(info->configFile, "r");
     }
     
+    if(info->flagcudaDeviceID) {
+    }
+    
     if(info->flagmode) {
     }
     
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.c b/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.c
index aebb323ac9..80ce6bb15e 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.c
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.c
@@ -38,7 +38,7 @@ static char __sccs_id[] = "@(#)pdb2mrc2d ver1.5; Date:96/11/02 @(#)";
 #include <stdlib.h>
 #include <string.h>
 #include <math.h>
-#undef DEBUG
+#define DEBUG
 #include "mrcImage.h"       
 #include "../inc/config.h"
 #include "pdbFile.h"
@@ -47,6 +47,10 @@ static char __sccs_id[] = "@(#)pdb2mrc2d ver1.5; Date:96/11/02 @(#)";
 #include "Matrix3D.h"
 #include "Map2D.h"
 
+#ifdef CUDA
+#include "eosCuda.h"
+#endif
+
 #define HowToCreateImageBit (0x1)
 #define HowToDrawMapBit     (0x2)
 
@@ -68,7 +72,13 @@ main(int argc, char* argv[])
     init0(&info);
     argCheck(&info, argc, argv);
     init1(&info);
-	
+
+#ifdef CUDA
+	if(info.flagcudaDeviceID) {
+		eosCudaInit(info.cudaDeviceID);
+	}
+#endif
+
 	linfo.dx = info.dx; linfo.dy = info.dy;
 	linfo.nx = info.nx; linfo.ny = info.ny;
 
@@ -147,7 +157,10 @@ main(int argc, char* argv[])
 					roty = ((double)iy)/info.rotny*2.0*M_PI; 
 					pdbRotationFollowingEulerAngle(&pdb, info.RotMode, -roty, rotx, -rotz); 
 				}
+
+				DEBUGPRINT3("rot: (%g %g %g) \n", rotx*DEGREE, roty*DEGREE, rotz*DEGREE);
 	    		lpdb2mrc2d(&mrc, &pdb,  &linfo, 'z', 0);
+
 				if(!info.flagRotMode) {
 					pdbRotationYXZ(&pdb, -rotx, roty, rotz);
 				} else {
@@ -159,6 +172,7 @@ main(int argc, char* argv[])
 					map2DCoordGet(&(to.x), &(to.y), roty, rotx, info.rotnx, info.rotny, ((info.mode&HowToDrawMapBit)>>1)); 
 					to.x = fmod(to.x*info.nx, out.HeaderN.x); 
 					to.y = fmod(to.y*info.ny, out.HeaderN.y); 
+					DEBUGPRINT2("map %f %f\n", to.x, to.y);
 					to.z = 0.0;
 					lmrcImageCopy(&out, &mrc, to);
 				} 
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.html b/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.html
index f600fecf44..fe13c09d0c 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.html
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.html
@@ -1 +1,49 @@
-/bin/bash: pdb2mrc2d: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdb2mrc2d</TITLE>
+</HEAD>
+<BODY>
+<H1>pdb2mrc2d</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdb2mrc2d
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(2D)
+    [-O[utput]           Out3D               (NULL      ).as(outFile             ) ] :Optional  :OutputDataFile(3D)
+    [-d[elta]            dx                  (5.0       ).as(Real                ) 
+                         dy                  (5.0       ).as(Real                ) ] :Essential :delta: dx[A] dy[A]
+    [-s[tart]            sx                  (0.0       ).as(Real                ) 
+                         sy                  (0.0       ).as(Real                ) ] :Optional  :start: startx[A] starty[A]: When -s was not set, image centre is the origin(0,0,0)
+    [-n[umber]           nx                  (0         ).as(Integer             ) 
+                         ny                  (0         ).as(Integer             ) ] :Essential :N:     nx ny (image size)
+    [-Rot[ation]         rotnx               (1         ).as(Integer             ) 
+                         rotny               (1         ).as(Integer             ) ] :Optional  :rotnx rotny
+    [-S[tart]            srotx               (0.0       ).as(Real                ) 
+                         sroty               (0.0       ).as(Real                ) 
+                         srotz               (0.0       ).as(Real                ) ] :Optional  :start(rotx roty rotz):ZXY
+    [-startE[uler]A[ngle]sRotMode            (YOYS      ).as(String              ) 
+                         sRot1               (0.0       ).as(Real                ) 
+                         sRot2               (0.0       ).as(Real                ) 
+                         sRot3               (0.0       ).as(Real                ) ] :Optional  :EulerAngle: Start Angle
+    [-E[uler]A[ngle]Mode RotMode             (YOYS      ).as(String              ) ] :Optional  :RotationMode
+    [-E[uler]A[ngle]Rot1 dRot1               (5.0       ).as(Real                ) 
+                         minRot1             (0.0       ).as(Real                ) 
+                         maxRot1             (180.0     ).as(Real                ) ] :Optional  :FirstRotation
+    [-E[uler]A[ngle]Rot2 dRot2               (5.0       ).as(Real                ) 
+                         minRot2             (0.0       ).as(Real                ) 
+                         maxRot2             (180.0     ).as(Real                ) ] :Optional  :SecondRotation
+    [-w[eight]           Weight              (1.0       ).as(Real                ) ] :Optional  :weight
+    [-sig[ma]            Sigma               (0.0       ).as(Real                ) ] :Optional  :Sigma[A]:Atom radius
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: 0 Merc; 1: Earth
+----- Attention1 -----
+If both of -s and -startEA, first -s and second -startEA will be performed
+----- Attention2 -----
+Bug fixed: rotation around x-axis. + is changed to - 
+----- Mode -----
+1: 0: equal angle 1: equal area
+2: 0: Mercatol    1: Morwide 
+</PRE>
+</BODY>
+</HTML>
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.pane b/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.pane
index c085a4130b..20e036233f 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.pane
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/pdb2mrc2d.pane
@@ -22,7 +22,8 @@
         -f 1 0 1 0 0 -1x1+1+19.500000 0 0 1.000000 0 0 0 'Weight' 'weight' w
         -f 1 0 1 0 0 -1x1+1+21.000000 0 0 0.000000 0 0 0 'Sigma' 'Sigma[A]:Atom radius' sig
         -I 1 0 1 0 0 1 -1x1+1+22.500000 ' ' 'configFile' 'ConfigurationFile' c
-        -i 1 0 1 0 0 -1x1+1+24.000000 0 0 0 0 0 'mode' 'Mode: 0 Merc; 1: Earth' m
+        -i 1 0 1 0 0 -1x1+1+24.000000 0 0 0 0 0 'cudaDeviceID' 'UseCuda' cuda
+        -i 1 0 1 0 0 -1x1+1+25.500000 0 0 0 0 0 'mode' 'Mode: 0 Merc; 1: Earth' m
     -E
   -E
 -E
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/test/Makefile b/src/Tools/pdbUtil/pdb2mrc2d/src/test/Makefile
index cedd45e25c..1a1e427fd6 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/test/Makefile
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/test/Makefile
@@ -14,4 +14,9 @@ exec:
 	../$(OSTYPE)/$(OBJECTNAME)  -i data/121p.shift.pdb -o data/121p.mrc2d -O data/121p.mrc2dStack -s -30 -30 -n 13 13 -d 5 5 -Rot 8 8  -m 3 -sig 3
 	@echo "----- Calc check -----"		
 
+exec2:
+	@echo "----- Execution Check -----"
+	../$(OSTYPE)/$(OBJECTNAME)  -i data/121p.shift.pdb -o data/121p.mrc2d2 -O data/121p.mrc2dStack2 -s -32 -32 -n 32 32 -d 2 2 -Rot 12 12 -m 1 -sig 3 
+	@echo "----- Calc check -----"		
+
 clean:
diff --git a/src/Tools/pdbUtil/pdb2mrc2d/src/usage.c b/src/Tools/pdbUtil/pdb2mrc2d/src/usage.c
index 4cb09f7eeb..e56bc61546 100755
--- a/src/Tools/pdbUtil/pdb2mrc2d/src/usage.c
+++ b/src/Tools/pdbUtil/pdb2mrc2d/src/usage.c
@@ -22,6 +22,7 @@ usage(char* thisProgram)
     fprintf(stderr, "    [-w[eight]           Weight              (1.0       ).as(Real                ) ] :Optional  :weight\n");
     fprintf(stderr, "    [-sig[ma]            Sigma               (0.0       ).as(Real                ) ] :Optional  :Sigma[A]:Atom radius\n");
     fprintf(stderr, "    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile\n");
+    fprintf(stderr, "    [-cuda               cudaDeviceID        (0         ).as(Integer             ) ] :Optional  :UseCuda\n");
     fprintf(stderr, "    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode: 0 Merc; 1: Earth\n");
     additionalUsage();
 }
-- 
2.11.0