-have_library: checking for main() in -lGL... -------------------- no
+have_library: checking for main() in -lGL... -------------------- yes
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lpthread -lrt -ldl -lcrypt -lm -lc"
-"xcrun clang -o conftest -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0/universal-darwin13 -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0 -I. -I/Users/tacyas/Eos/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -g -Os -pipe conftest.c -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib -L/usr/lib -L/Users/tacyas/Eos/lib/X86MAC64 -L/Users/tacyas/Eos/util/X86MAC64/lib -L. -L/usr/local/lib -arch x86_64 -arch i386 -lruby.2.0.0 -lpthread -ldl -lobjc "
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lpthread -lrt -ldl -lcrypt -lm -lc"
+/home/people/tacyas/Eos/util/X86LINUX64/lib/ruby/1.9.1/mkmf.rb:305: warning: Insecure world writable dir /net/fs08/workFS08 in PATH, mode 040777
checked program was:
/* begin */
1: #include "ruby.h"
2:
-3: int main(int argc, char **argv)
-4: {
-5: return 0;
-6: }
+3: int main() {return 0;}
/* end */
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
-"xcrun clang -o conftest -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0/universal-darwin13 -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0 -I. -I/Users/tacyas/Eos/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -g -Os -pipe conftest.c -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib -L/usr/lib -L/Users/tacyas/Eos/lib/X86MAC64 -L/Users/tacyas/Eos/util/X86MAC64/lib -L. -L/usr/local/lib -arch x86_64 -arch i386 -lruby.2.0.0 -lGL -lpthread -ldl -lobjc "
-conftest.c:5:57: error: use of undeclared identifier 'main'
-int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- ^
-1 error generated.
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
checked program was:
/* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
+1: #include "ruby.h"
+2:
+3: /*top*/
+4: int main() {return 0;}
+5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
+/* end */
+
+--------------------
+
+have_library: checking for main() in -lGLU... -------------------- yes
+
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
+checked program was:
+/* begin */
+1: #include "ruby.h"
+2:
+3: /*top*/
+4: int main() {return 0;}
+5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
+/* end */
+
+--------------------
+
+have_library: checking for main() in -lglut... -------------------- yes
+
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
+checked program was:
+/* begin */
+1: #include "ruby.h"
+2:
+3: /*top*/
+4: int main() {return 0;}
+5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
+/* end */
+
+--------------------
+
+have_library: checking for main() in -ltcl... -------------------- yes
+
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
+checked program was:
+/* begin */
+1: #include "ruby.h"
+2:
+3: /*top*/
+4: int main() {return 0;}
+5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
+/* end */
+
+--------------------
+
+have_library: checking for main() in -ltk... -------------------- yes
+
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
+checked program was:
+/* begin */
+1: #include "ruby.h"
+2:
+3: /*top*/
+4: int main() {return 0;}
+5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
+/* end */
+
+--------------------
+
+have_library: checking for main() in -lBLT... -------------------- yes
+
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
+checked program was:
+/* begin */
+1: #include "ruby.h"
+2:
+3: /*top*/
+4: int main() {return 0;}
+5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
/* end */
-"xcrun clang -o conftest -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0/universal-darwin13 -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0/ruby/backward -I/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/include/ruby-2.0.0 -I. -I/Users/tacyas/Eos/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -g -Os -pipe conftest.c -L. -L/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib -L/usr/lib -L/Users/tacyas/Eos/lib/X86MAC64 -L/Users/tacyas/Eos/util/X86MAC64/lib -L. -L/usr/local/lib -arch x86_64 -arch i386 -lruby.2.0.0 -lGL -lpthread -ldl -lobjc "
-conftest.c:5:15: warning: implicit declaration of function 'main' is invalid in C99 [-Wimplicit-function-declaration]
-int t(void) { main(); return 0; }
- ^
-1 warning generated.
-ld: library not found for -lGL
-conftest.c:5:15: warning: implicit declaration of function 'main' is invalid in C99 [-Wimplicit-function-declaration]
-int t(void) { main(); return 0; }
- ^
-1 warning generated.
-clang: error: linker command failed with exit code 1 (use -v to see invocation)
+--------------------
+
- have_library: checking for main() in -lasound... -------------------- no
++have_library: checking for main() in -lasound... -------------------- yes
+
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -lBLT -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
- /usr/bin/ld: cannot find -lasound
- collect2: ld はステータス 1 で終了しました
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lBLT -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
+checked program was:
+/* begin */
+1: #include "ruby.h"
+2:
+3: /*top*/
+4: int main() {return 0;}
+5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
+/* end */
+
- "gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64ICC -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64ICC -L/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64ICC/lib -L. -rdynamic -Wl,-export-dynamic -lBLT -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
- /usr/bin/ld: cannot find -lasound
- collect2: ld はステータス 1 で終了しました
++--------------------
++
++have_library: checking for main() in -lgif... -------------------- yes
++
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
+ checked program was:
+ /* begin */
- 1: #include "ruby.h"
- 2:
- 3: /*top*/
- 4: extern int t(void);
- 5: int t(void) { main(); return 0; }
- 6: int main(int argc, char **argv)
- 7: {
- 8: if (argc > 1000000) {
- 9: printf("%p", &t);
-10: }
-11:
-12: return 0;
-13: }
++1: #include "ruby.h"
++2:
++3: /*top*/
++4: int main() {return 0;}
++5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
++/* end */
++
++--------------------
++
++have_library: checking for main() in -lfftw3f... -------------------- yes
++
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++checked program was:
++/* begin */
++1: #include "ruby.h"
++2:
++3: /*top*/
++4: int main() {return 0;}
++5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
++/* end */
++
++--------------------
++
++have_library: checking for main() in -lnr... -------------------- yes
++
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lnr -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++checked program was:
++/* begin */
++1: #include "ruby.h"
++2:
++3: /*top*/
++4: int main() {return 0;}
++5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
++/* end */
++
++--------------------
++
++have_library: checking for main() in -lnl... -------------------- no
++
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lnr -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lnl -lnr -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++/usr/bin/ld: cannot find -lnl
++collect2: ld returned 1 exit status
++checked program was:
++/* begin */
++1: #include "ruby.h"
++2:
++3: /*top*/
++4: int main() {return 0;}
++5: int t() { void ((*volatile p)()); p = (void ((*)()))main; return 0; }
++/* end */
++
++"gcc -o conftest -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/x86_64-linux -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1/ruby/backward -I/home/people/tacyas/Eos/util/X86LINUX64/include/ruby-1.9.1 -I. -I/home/people/tacyas/Eos/include -O3 -ggdb -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-missing-field-initializers -Wno-long-long conftest.c -L. -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L/usr/lib -Wl,-R/usr/lib -L/home/people/tacyas/Eos/lib/X86LINUX64 -Wl,-R/home/people/tacyas/Eos/lib/X86LINUX64 -L/home/people/tacyas/Eos/util/X86LINUX64/lib -Wl,-R/home/people/tacyas/Eos/util/X86LINUX64/lib -L. -rdynamic -Wl,-export-dynamic -lnr -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -Wl,-R -Wl,/home/people/tacyas/Eos/util/X86LINUX64/lib -L/home/people/tacyas/Eos/util/X86LINUX64/lib -lruby-static -lnl -lnr -lfftw3f -lgif -lasound -lBLT -ltk -ltcl -lglut -lGLU -lGL -lpthread -lrt -ldl -lcrypt -lm -lc"
++/usr/bin/ld: cannot find -lnl
++collect2: ld returned 1 exit status
+checked program was:
+/* begin */
+1: #include "ruby.h"
+2:
+3: /*top*/
+4: int main() {return 0;}
+5: int t() { main(); return 0; }
/* end */
--------------------
SWIGINTERN VALUE
--_wrap_lmrcImageDevidedByImage(int argc, VALUE *argv, VALUE self) {
++_wrap_lmrcImageDividedByImage(int argc, VALUE *argv, VALUE self) {
mrcImage *arg1 = (mrcImage *) 0 ;
mrcImage *arg2 = (mrcImage *) 0 ;
mrcImage *arg3 = (mrcImage *) 0 ;
}
res1 = SWIG_ConvertPtr(argv[0], &argp1,SWIGTYPE_p_mrcImage, 0 | 0 );
if (!SWIG_IsOK(res1)) {
-- SWIG_exception_fail(SWIG_ArgError(res1), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDevidedByImage", 1, argv[0] ));
++ SWIG_exception_fail(SWIG_ArgError(res1), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDividedByImage", 1, argv[0] ));
}
arg1 = (mrcImage *)(argp1);
res2 = SWIG_ConvertPtr(argv[1], &argp2,SWIGTYPE_p_mrcImage, 0 | 0 );
if (!SWIG_IsOK(res2)) {
-- SWIG_exception_fail(SWIG_ArgError(res2), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDevidedByImage", 2, argv[1] ));
++ SWIG_exception_fail(SWIG_ArgError(res2), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDividedByImage", 2, argv[1] ));
}
arg2 = (mrcImage *)(argp2);
res3 = SWIG_ConvertPtr(argv[2], &argp3,SWIGTYPE_p_mrcImage, 0 | 0 );
if (!SWIG_IsOK(res3)) {
-- SWIG_exception_fail(SWIG_ArgError(res3), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDevidedByImage", 3, argv[2] ));
++ SWIG_exception_fail(SWIG_ArgError(res3), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDividedByImage", 3, argv[2] ));
}
arg3 = (mrcImage *)(argp3);
-- lmrcImageDevidedByImage(arg1,arg2,arg3);
++ lmrcImageDividedByImage(arg1,arg2,arg3);
return Qnil;
fail:
return Qnil;
SWIGINTERN VALUE
--_wrap_lmrcImageDevidedByReal(int argc, VALUE *argv, VALUE self) {
++_wrap_lmrcImageDividedByReal(int argc, VALUE *argv, VALUE self) {
mrcImage *arg1 = (mrcImage *) 0 ;
double arg2 ;
void *argp1 = 0 ;
}
res1 = SWIG_ConvertPtr(argv[0], &argp1,SWIGTYPE_p_mrcImage, 0 | 0 );
if (!SWIG_IsOK(res1)) {
-- SWIG_exception_fail(SWIG_ArgError(res1), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDevidedByReal", 1, argv[0] ));
++ SWIG_exception_fail(SWIG_ArgError(res1), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDividedByReal", 1, argv[0] ));
}
arg1 = (mrcImage *)(argp1);
ecode2 = SWIG_AsVal_double(argv[1], &val2);
if (!SWIG_IsOK(ecode2)) {
-- SWIG_exception_fail(SWIG_ArgError(ecode2), Ruby_Format_TypeError( "", "double","lmrcImageDevidedByReal", 2, argv[1] ));
++ SWIG_exception_fail(SWIG_ArgError(ecode2), Ruby_Format_TypeError( "", "double","lmrcImageDividedByReal", 2, argv[1] ));
}
arg2 = (double)(val2);
-- lmrcImageDevidedByReal(arg1,arg2);
++ lmrcImageDividedByReal(arg1,arg2);
return Qnil;
fail:
return Qnil;
SWIGINTERN VALUE
--_wrap_lmrcImageDevidedByRealForOnlyPositive(int argc, VALUE *argv, VALUE self) {
++_wrap_lmrcImageDividedByRealForOnlyPositive(int argc, VALUE *argv, VALUE self) {
mrcImage *arg1 = (mrcImage *) 0 ;
double arg2 ;
void *argp1 = 0 ;
}
res1 = SWIG_ConvertPtr(argv[0], &argp1,SWIGTYPE_p_mrcImage, 0 | 0 );
if (!SWIG_IsOK(res1)) {
-- SWIG_exception_fail(SWIG_ArgError(res1), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDevidedByRealForOnlyPositive", 1, argv[0] ));
++ SWIG_exception_fail(SWIG_ArgError(res1), Ruby_Format_TypeError( "", "mrcImage *","lmrcImageDividedByRealForOnlyPositive", 1, argv[0] ));
}
arg1 = (mrcImage *)(argp1);
ecode2 = SWIG_AsVal_double(argv[1], &val2);
if (!SWIG_IsOK(ecode2)) {
-- SWIG_exception_fail(SWIG_ArgError(ecode2), Ruby_Format_TypeError( "", "double","lmrcImageDevidedByRealForOnlyPositive", 2, argv[1] ));
++ SWIG_exception_fail(SWIG_ArgError(ecode2), Ruby_Format_TypeError( "", "double","lmrcImageDividedByRealForOnlyPositive", 2, argv[1] ));
}
arg2 = (double)(val2);
-- lmrcImageDevidedByRealForOnlyPositive(arg1,arg2);
++ lmrcImageDividedByRealForOnlyPositive(arg1,arg2);
return Qnil;
fail:
return Qnil;
rb_define_module_function(mMolvieRuby, "IsFT", _wrap_IsFT, -1);
rb_define_module_function(mMolvieRuby, "IsFFT", _wrap_IsFFT, -1);
rb_define_module_function(mMolvieRuby, "mrcImageInfoSet", _wrap_mrcImageInfoSet, -1);
-- rb_define_module_function(mMolvieRuby, "lmrcImageDevidedByImage", _wrap_lmrcImageDevidedByImage, -1);
++ rb_define_module_function(mMolvieRuby, "lmrcImageDividedByImage", _wrap_lmrcImageDividedByImage, -1);
rb_define_module_function(mMolvieRuby, "lmrcImagetMapForZero", _wrap_lmrcImagetMapForZero, -1);
rb_define_module_function(mMolvieRuby, "lmrcImageSN", _wrap_lmrcImageSN, -1);
-- rb_define_module_function(mMolvieRuby, "lmrcImageDevidedByReal", _wrap_lmrcImageDevidedByReal, -1);
-- rb_define_module_function(mMolvieRuby, "lmrcImageDevidedByRealForOnlyPositive", _wrap_lmrcImageDevidedByRealForOnlyPositive, -1);
++ rb_define_module_function(mMolvieRuby, "lmrcImageDividedByReal", _wrap_lmrcImageDividedByReal, -1);
++ rb_define_module_function(mMolvieRuby, "lmrcImageDividedByRealForOnlyPositive", _wrap_lmrcImageDividedByRealForOnlyPositive, -1);
rb_define_module_function(mMolvieRuby, "lmrcImageAddedByReal", _wrap_lmrcImageAddedByReal, -1);
rb_define_module_function(mMolvieRuby, "lmrcImageStdDev", _wrap_lmrcImageStdDev, -1);
rb_define_module_function(mMolvieRuby, "lmrcImageStdErr", _wrap_lmrcImageStdErr, -1);
<PRE>
../src/decoder.c:
++<<<<<<< HEAD
++=======
+ ../src/gifcompr.c:
+
+ ../src/gifencod.c:
+
++>>>>>>> FETCH_HEAD
../src/gifFileInit.c:
../src/gifFileWrite.c:
../src/gifUtil.c:
++<<<<<<< HEAD
+../src/gifcompr.c:
+
+../src/gifencod.c:
+
++=======
++>>>>>>> FETCH_HEAD
../src/lmrc2gif.c:
</PRE>
<HR>
../src/lmolvieLight.c:
++<<<<<<< HEAD
+../src/lmolvieMRCread.c:
+
++=======
++>>>>>>> FETCH_HEAD
../src/lmolvieMouse.c:
../src/lmolvieMouseDrive.c:
../src/lmolvieMouseParallel.c:
++<<<<<<< HEAD
++=======
+ ../src/lmolvieMRCread.c:
+
++>>>>>>> FETCH_HEAD
../src/lmolvieMrcViewerDisplay.c:
../src/lmolvieMrcViewerKeyboard.c:
<PRE>
../src/psFileCircle.c:
++<<<<<<< HEAD
+../src/psFileContour.c:
+
+../src/psFileContour3D.c:
+
++=======
+ ../src/psFileContour3D.c:
+
+ ../src/psFileContour.c:
+
++>>>>>>> FETCH_HEAD
../src/psFileEnd.c:
../src/psFileImage.c:
../src/ctfInfoRead.c:
++<<<<<<< HEAD
+../src/ctfInfoWrite.c:
+
+../src/ctfInfoWrite2.c:
+
++=======
+ ../src/ctfInfoWrite2.c:
+
+ ../src/ctfInfoWrite.c:
+
++>>>>>>> FETCH_HEAD
../src/ctfWeight.c:
../src/ctfZeroPoint.c:
<PRE>
../src/llDataCheck.c:
++<<<<<<< HEAD
+../src/llDataETC.c:
+
+../src/llDataError.c:
+
++=======
+ ../src/llDataError.c:
+
+ ../src/llDataETC.c:
+
++>>>>>>> FETCH_HEAD
../src/llDataGet.c:
../src/llDataInfo.c:
../src/lllDataAvgTo.c:
++<<<<<<< HEAD
+../src/lllDataAxisSearch.c:
+
++=======
++>>>>>>> FETCH_HEAD
../src/lllDataAxisSearch2.c:
../src/lllDataAxisSearchAndAverage.c:
++<<<<<<< HEAD
+../src/lllDataCTFCompensate.c:
+
+../src/lllDataCTFObservation.c:
++=======
+ ../src/lllDataAxisSearch.c:
++>>>>>>> FETCH_HEAD
../src/lllDataCompare.c:
../src/lllDataContributionCalcDifferentN.c:
++<<<<<<< HEAD
++=======
+ ../src/lllDataCTFCompensate.c:
+
+ ../src/lllDataCTFObservation.c:
+
++>>>>>>> FETCH_HEAD
../src/lllDataDifferenceCalc.c:
../src/lllDataEquatorAdd.c:
../src/lllDataExtract.c:
++<<<<<<< HEAD
+../src/lllDataFit.c:
+
++=======
++>>>>>>> FETCH_HEAD
../src/lllDataFit2.c:
../src/lllDataFitAndAverage.c:
++<<<<<<< HEAD
++=======
+ ../src/lllDataFit.c:
+
++>>>>>>> FETCH_HEAD
../src/lllDataFitMergedLL.c:
../src/lllDataFitOut.c:
../src/lllDataRescaling.c:
++<<<<<<< HEAD
+../src/lllDataSingleCTFCompensation.c:
+
+../src/lllDataWeightSet.c:
+
+../src/lllDatarMaxLimit.c:
++=======
+ ../src/lllDatarMaxLimit.c:
+
+ ../src/lllDataSingleCTFCompensation.c:
+
+ ../src/lllDataWeightSet.c:
++>>>>>>> FETCH_HEAD
</PRE>
<HR>
<A NAME="include">
../src/lEvaluateCorrelationMapwithCommonLine.c:
++<<<<<<< HEAD
++=======
+ ../src/lFETmapOrientationSearchBySimultaneousFitting.c:
+
++>>>>>>> FETCH_HEAD
../src/lFETOrientationSearchByAnnealing.c:
../src/lFETOrientationSearchByFeatureAlignment.c:
../src/lFETOrientationSearchByFeatureAlignmentSphere.c:
++<<<<<<< HEAD
+../src/lFETmapOrientationSearchBySimultaneousFitting.c:
+
++=======
++>>>>>>> FETCH_HEAD
../src/lFETsmallMapSetCreate_forSimultaneousMinimization.c:
../src/lInitialDataFileRead.c:
../src/lLcalculation.c:
++<<<<<<< HEAD
+../src/lPlaneRotationAngleSet.c:
++=======
+ ../src/lllDatarMaxLimitForSeparation.c:
++>>>>>>> FETCH_HEAD
../src/lllDataSeparationInfoPrint.c:
../src/lllDataSeparationInfoSet.c:
++<<<<<<< HEAD
+../src/lllDatarMaxLimitForSeparation.c:
+
++=======
++>>>>>>> FETCH_HEAD
../src/lllExtract.c:
../src/lllExtractCtfinfFileCreate.c:
++<<<<<<< HEAD
+../src/lllExtractWithSeparation.c:
+
+../src/lllExtractdYEstimate.c:
+
++=======
+ ../src/lllExtractdYEstimate.c:
+
+ ../src/lllExtractWithSeparation.c:
+
++>>>>>>> FETCH_HEAD
../src/lmrc2Dto3D.c:
../src/lmrc2Dto3DSIRT.c:
../src/lmrcImageOneLineGet.c:
../src/lmrcImageSinogramCorrelationAdditionalWeight.c:
++<<<<<<< HEAD
++=======
+
+ ../src/lPlaneRotationAngleSet.c:
++>>>>>>> FETCH_HEAD
</PRE>
<HR>
<A NAME="include">
<PRE>
../src/matrix3DEulerAngleGet.c:
++<<<<<<< HEAD
+../src/matrix3DEulerAngleSet.c:
+
+../src/matrix3DEulerAngles.c:
+
++=======
+ ../src/matrix3DEulerAngles.c:
+
+ ../src/matrix3DEulerAngleSet.c:
+
++>>>>>>> FETCH_HEAD
../src/matrix3DFile.c:
../src/matrix3DInit.c:
<H2>Information from source codes</H2>
</A>
<PRE>
++<<<<<<< HEAD
++=======
+ ../src/lVectorSpline2D.c:
+
++>>>>>>> FETCH_HEAD
../src/Vector.c:
../src/VectorRead.c:
../src/VectorScalarProduct.c:
++<<<<<<< HEAD
+
+../src/lVectorSpline2D.c:
++=======
++>>>>>>> FETCH_HEAD
</PRE>
<HR>
<A NAME="include">
++<<<<<<< HEAD
+/bin/bash: dcdAtomChangeDistanceFromAtom: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>dcdAtomChangeDistanceFromAtom</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>dcdAtomChangeDistanceFromAtom</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: dcdAtomChangeDistanceFromAtom
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: dcdAtomDistanceDistribution: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>dcdAtomDistanceDistribution</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>dcdAtomDistanceDistribution</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: dcdAtomDistanceDistribution
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-o[utput]mrc OutMRC (NULL )] :Optional :Output: MRCFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: dcdFilePrint: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>dcdFilePrint</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>dcdFilePrint</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: dcdFilePrint
+ Options:
+ [-i[nput] In (NULL )] :Essential :Input: DCD
+ [-i[nput]p[db] InPDB (NULL )] :Optional :Input: PDB
+ [-o[utput] Out (NULL )] :Essential :Output: ASCII
+ [-o[utput]p[db] OutPDB (NULL )] :Optional :Output: PDB
+ [-r[ange] rStart (10 )rEnd (100 )rDelta (10 )] :Optional :Input: Start End Delta
+ [-s[tart] Start (10 )] :Optional :Input: Start
+ [-e[nd] End (100 )] :Optional :Input: End
+ [-d[elta] Delta (10 )] :Optional :Input: Delta(Interval)
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: dcdInfo: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>dcdInfo</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>dcdInfo</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: dcdInfo
+ Options:
+ [-i[nput] In (NULL )] :Essential :Input: DCD
+ [-i[nput]p[db] InPDB (NULL )] :Optional :Input: PDB
+ [-o[utput] Out (NULL )] :Essential :Output: ASCII
+ [-o[utput]p[db] OutPDB (NULL )] :Optional :Output: PDB
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: dcdSelectAtoms: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>dcdSelectAtoms</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>dcdSelectAtoms</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: dcdSelectAtoms
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: dcdSerectAtom: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>dcdSerectAtom</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>dcdSerectAtom</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: dcdSerectAtom
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: dcdTimeSeriesBehavior: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>dcdTimeSeriesBehavior</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>dcdTimeSeriesBehavior</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: dcdTimeSeriesBehavior
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: Display2: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>Display2</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>Display2</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: Display2
+ Options:
+ [-i[nput] In (NULL )] :Optional :InputDataFile
+ <<<<<<< HEAD
+ [-t[epmlate] Template (85.roi )] :Optional :Template for InputFile
+ =======
+ [-t[epmlate] Template (2100635408.roi )] :Optional :Template for InputFile
+ >>>>>>> FETCH_HEAD
+ [-H[ighForThres] ThresHigh (0.0 )] :Optional :Template for InputFile
+ [-L[owForThres] ThresLow (0.0 )] :Optional :Template for InputFile
+ [-Zoom Zoom (1.0 )] :Optional :Zoom for InputFile
+ [-Inverse ] :Optional :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile
+ [-o[utput] Out (.EosLog )] :Optional :OutputLogFile
+ [-display geometry (:0.0 )] :Optional :OutputLogFile
+ [-geometry display (1024x1024+0+0)] :Optional :OutputLogFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ New wish commands of Display2
+ mrcInfoSet [z|min|max] value
+ mrcInfoSet [log|pow]
+ mrcInfoGet [Nx|Ny|Nz|Max|Min|Mean|Hist]
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: StereoDisplay: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>StereoDisplay</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>StereoDisplay</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: StereoDisplay
+ Options:
+ [-il[nputl] Inl (NULL )] :Optional :Input: Left
+ [-ir[nputr] Inr (NULL )] :Optional :Input: Right
+ [-I[nputFileList] In (NULL )] :Optional :Input: Left Right
+ [-o[utput] Out (NULL )] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ >>> -I for InFileList
+ Left1 Right1
+ Left2 Right2
+ .....
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: homology2PG: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>homology2PG</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>homology2PG</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: homology2PG
+ Options:
+ [-i[nput] In (stdin )] :Essential :InputDataFile
+ [-o[utput] Out (stdout )] :Optional :OutputDataFile
+ [-skip Skip (0 )] :Optional :SkipResidueNumber
+ [-H[ost] Host (pc00 )] :Optional :HostName
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-P[ort] Port (5432 )] :Optional :Port
+ [-d[atabase] database (test )] :Optional :database
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pgJournalSelect: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pgJournalSelect</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pgJournalSelect</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pgJournalSelect
+ Options:
+ [-i[nput] In (NULL )] :Optional :InputDataFile
+ [-o[utput] Out (stdout )] :Optional :OutputDataFile
+ [-H[ost] Host (pc00 )] :Optional :HostName
+ [-P[ort] Port (5432 )] :Optional :Port
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pgSelect: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pgSelect</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pgSelect</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pgSelect
+ Options:
+ [-H[ostname] hostname (pc17 )] :Optional :hostname
+ [-o[utput] Out (NULL )] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ [-P[ortNumber] port (7777 )] :Optional :port
+ [-D[ataBaseName] dbName (test )] :Optional :dbName
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: mrcImageDensityInfo: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>mrcImageDensityInfo</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>mrcImageDensityInfo</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: mrcImageDensityInfo
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (stdout )] :Optional :OutputDataFile
+ [-C[ontour] Contour (10 )] :Optional :ContourLevel: 10 2.901940e-307ach
+ [-log Log (NULL )] :Optional :OutputDataFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Attention !!!-----
+ In Eos system, positive values are regarded as density.
+ If a pixel has a negative value, the value of the pixel is regarded as zero.lmrcImageDensityInfo Mode:
+ 1: PercentageVolume
+ 2: CentreOfGravity
+ 4: Max
+ 8: SD around CentreOfGravity
+ 16: SD around Max
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: mrcImageSphereCheck: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>mrcImageSphereCheck</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>mrcImageSphereCheck</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: mrcImageSphereCheck
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: mrcImageSplit: そのようなファイルやディレクトリはありません
++=======
+ 1th word not found in : exception
+ <HTML>
+ <HEAD>
+ <TITLE>mrcImageSplit</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>mrcImageSplit</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: mrcImageSplit
+ Options:
+ [-i[nput] In (NULL )] :Essential :Input: mrcImage
+ [-o[utput] Out ( )] :Optional :Output: Basename
+ [-s[uffix] Suffix (008830078720000.splt)] :Optional :Output: Suffix
+ [-H[eight] Height (0 )] :Optional :Input: Height[y]: SplitSize [pixel]
+ [-W[idth] Width (0 )] :Optional :Input: Width[x]: SplitSize [pixel]
+ [-S[ection] Section (0 )] :Optional :Input: Section[z]: SplitSize [pixel]
+ [-H[eight]A[ngstrom] HeightA (0 )] :Optional :Input: Height: SplitSize [A]
+ [-W[idth]A[ngstrom] WidthA (0 )] :Optional :Input: Width: SplitSize [A]
+ [-S[ection]A[ngstrom]SectionA (0 )] :Optional :Input: Section: SplitSize [A]
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: mrcImageSuperResolution: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>mrcImageSuperResolution</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>mrcImageSuperResolution</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: mrcImageSuperResolution
+ Options:
+ [-I[nput] InOriginal (NULL )] :Essential :Input: Original
+ [-i[nput] InPrevious (NULL )] :Essential :Input: Previous
+ [-i[nput]c[ounter] FFTInCount (NULL )] :Optional :Input: CounterforWeight FourierSpace
+ [-o[utput] Out (NULL )] :Essential :Output: Next
+ [-t[ime] t (1 )] :Optional :Number of time: Iteration(Real Space)
+ [-fromp[oint]1 x00 (0 )y00 (0 )z00 (0 )] :Optional :First value near origin of coordinates: x00[pixel] y00[pixel] z00[pixel]
+ [-top[oint]1 x01 (2 )y01 (2 )z01 (2 )] :Optional :target value: x01[pixel] y01[pixel] z01[pixel]
+ [-fromp[oint]2 x10 (0 )y10 (0 )z10 (0 )] :Optional :First value far from origin of coordinates: x10[pixel] y10[pixel] z10[pixel]
+ [-top[oint]2 x11 (0 )y11 (0 )z11 (0 )] :Optional :target value: x11[pixel] y11[pixel] z11[pixel]
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Essential :RealSpaceCalculating
+ [-LabelingMode labelingmode (0 )] :Optional :LabelingMode
+ [-max[value] max (800 )] :Optional :Density Max value:Support Constraint(%)
+ [-min[value] min (200 )] :Optional :Density Min value:Support Constraint(%)
+ [-sh[ape] shape (0 )] :Optional :Shape:0(Rectangule),1(Globe)
+ [-h[alf]v[alue]p[oint]hvp (0.0 )] :Optional :Half value point(/[A])
+ [-Inverse ] :Optional :Inverse
+ [-nM[olecule] nMolecule (1 )] :Optional :Number of Molecule
+ [-M[olecularWeight] MolecularWeight (80000 )] :Optional :MolecularWeight
+ [-D[ensity] Density (1.35 )] :Optional :Density(g/cm3)
+ [-counter incounter (3.0 )] :Optional :Counter(Fourier Space)
+ [-d[elta]Density deltaDens (100.0 )] :Optional :Delta (Convergence)
+ [-d[elta]Area deltaArea (100.0 )] :Optional :Area (Convergence)
+ [-sub[traction] sub (0.2 )] :Optional :Subtraction(Convergence)
+ [-ratio ratio (0.3 )] :Optional :Ratio(Convergence)
+ [-t[ime]max tmax (1000 )] :Optional :Time Max(Convergence)
+ [-w[eight]d[elta] WeightDelta (0.1 )] :Optional :WeightDelta(Fourier Space)
+ [-w[eight]m[ax] WeightMax (2 )] :Optional :WeightMax(Fourier Space)
+ [-Subtraction ] :Optional :Subtraction(Real Space)
+ ----- Additional Usage -----
+ -m Option
+ 1 : AreaAndLocation
+ 2 : Density
+ 3 : AreaAndLocationandDensity
+ +4 : Convergence(Option)
+ +16 : NonnegativeMode(before RealSpaceConstraint)
+ +32 : Binarization(before RealSpaceConstraint)
+ +64 : Labeling
+ +128 : SixOrientation
+ +256 : LowpassfilterMode(-hvp is required)
+ +512 : CounterMode(-ic is required)
+ -----------------------------------------------------
+ -Inverse
+ If high density means the location of protein, -Inverse is required for volume calculation.
+ -wm and -wd
+ weight = counter / (weightmax + counter)
+ weightmax -> 0 (weightdelt by weightdelta)
+ -LabelinMode
+ 0 : TheLargestLabelingSearch
+ 1 : SomeVolumeLabelingSearch
+ -Subtraction
+ Real Space Constraint for desolving edge problem
+
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: mrcImageVolumeCalc: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>mrcImageVolumeCalc</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>mrcImageVolumeCalc</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: mrcImageVolumeCalc
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (stdout )] :Optional :OutputDataFile
+ [-n[Molecule] nMolecule (1.0 )] :Optional :NumberOfMolecule
+ [-M[olecularWeight] MolecularWeight (1.0 )] :Optional :MolecularWeight
+ [-d[ensty] Density (1.35 )] :Optional :Density
+ [-D[elta] Delta (5.0 )] :Optional :Delta[A]
+ [-R[ange] MinVol (0.0 )MaxVol (200.0 )DeltaVol (10.0 )] :Optional :vol%
+ [-I[nverse] ] :Optional :Inverse
+ [-format Format (ContourLevel(%3g): %g %lu)] :Optional :Format
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ -format
+ 1st double # ContourLevel[%]
+ 2nd double # Contour[value]
+ 3rd int # VolumeNumber [fromBlack]
+ 4th int # VolumeNumber [fromWhite] ; Default : omiited
+ 5th double # Volume[A^3] ; Default : omitted
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: mrcImageWindowing: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>mrcImageWindowing</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>mrcImageWindowing</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: mrcImageWindowing
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-W[indowing] Wx (0.1 )WxMax (0.0 )Wy (0.1 )WyMax (0.0 )] :Optional :Windowsing Size:
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ >>> Mode
+ 0: If 0<x<0.1*nx or 0.9*nx<x<nx, then cos windowing, else original.
+ 0: 90% windowing: fixed.
+ 1: Wy: Settings: variable.
+ 2: WxMax and Wx
+ WyMax and Wy Settings: variables
+ x/Nx < WxMax or 1-WxMax < x/Nx : 0
+ WxMax < x/Nx < Wx or 1-Wx < x/Nx < 1-WxMax : cos window
+ Wx < x/Nx < 1-Wx : 1
+ Wy and WyMax are also used for windowing in the similar manner.
+ +0 : To Zero.
+ +16: Contrast down around mean.
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: mrcSinogramFETsmoothParameterMatching: そのようなファイルやディレクトリはありません
++=======
+ /bin/bash: mrcSinogramFETsmoothParameterMatching: No such file or directory
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdb2mrc2d: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdb2mrc2d</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdb2mrc2d</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdb2mrc2d
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Optional :OutputDataFile(2D)
+ [-O[utput] Out3D (NULL )] :Optional :OutputDataFile(3D)
+ [-d[elta] dx (5.0 )dy (5.0 )] :Essential :delta: dx[A] dy[A]
+ [-s[tart] sx (0.0 )sy (0.0 )] :Optional :start: startx[A] starty[A]: When -s was not set, image centre is the origin(0,0,0)
+ [-n[umber] nx (0 )ny (0 )] :Essential :N: nx ny (image size)
+ [-Rot[ation] rotnx (1 )rotny (1 )] :Optional :rotnx rotny
+ [-S[tart] srotx (0.0 )sroty (0.0 )srotz (0.0 )] :Optional :start(rotx roty rotz):ZXY
+ [-startE[uler]A[ngle]sRotMode (YOYS )sRot1 (0.0 )sRot2 (0.0 )sRot3 (0.0 )] :Optional :EulerAngle: Start Angle
+ [-E[uler]A[ngle]Mode RotMode (YOYS )] :Optional :RotationMode
+ [-E[uler]A[ngle]Rot1 dRot1 (5.0 )minRot1 (0.0 )maxRot1 (180.0 )] :Optional :FirstRotation
+ [-E[uler]A[ngle]Rot2 dRot2 (5.0 )minRot2 (0.0 )maxRot2 (180.0 )] :Optional :SecondRotation
+ [-w[eight] Weight (1.0 )] :Optional :weight
+ [-sig[ma] Sigma (0.0 )] :Optional :Sigma[A]:Atom radius
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :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>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbChargeFit: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbChargeFit</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbChargeFit</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbChargeFit
+ Options:
+ [-i[nput]f[ixed pdb] InFix (NULL )] :Essential :InputFixedPdbFile
+ [-i[nput]m[oved pdb] InMove (NULL )] :Essential :InputMovedPdbFile
+ [-o[utput] OutTxt (NULL )] :Essential :OutputTextFile
+ [-s[ymmetry of helix(degree/A)]symmetry (0.47096 )] :Optional :default: 13/28
+ [-zmin zmin (-28 )] :Optional :minimum z
+ [-zmax zmax (28 )] :Optional :maximum z
+ [-zDel[ta] zDel (1 )] :Optional :delta z
+ [-mind[istance] mind (1 )] :Optional :set atoms distance to mind
+ [-maxd[istance] maxd (5 )] :Optional :ignore atoms distance
+ [-a[xis coordinate] axisX (70 )axisY (70 )] :Optional :(x, y)
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Algorythm -----
+ score = Sum(1/SQR(length))
+ , where length is the set of length between charged atoms
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbCrystalCreate: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbCrystalCreate</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbCrystalCreate</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbCrystalCreate
+ Options:
+ [-i[nput] In (NULL )] :Essential :Input:PDB
+ [-I[nfo] Info (NULL )] :Essential :Input:Crystal Information
+ [-o[utput] Out (NULL )] :Essential :Output:PDB
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ ----- CrystalInfo -----
+ aAxis %15.6g %15.6g %15.6g
+ bAxis %15.6g %15.6g %15.6g
+ cAxis %15.6g %15.6g %15.6g
+ CellLength %15.6g %15.6g %15.6g
+ Origin %15.6g %15.6g %15.6g
+ N %15d %15d %15d
+ StartN %15d %15d %15d
+ SpaceGroup %15d
+ HelixInfo %10d %10d %10d
+ ### Attention ###
+ Parameter Order is important: Dependent between CellLength and a|b|cAxis.
+ Because each of aAxis, bAxis, cAxis must be a unit vector.
+ HelixInfo t u n
+ ----- CrystalSpaceGroup -----
+ 0 P1
+ 1 HelicalSymmmetry
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbHelix: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbHelix</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbHelix</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbHelix
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Optional :OutputDataFile
+ [-3[D] Out3D (NULL )] :Optional :OutputDataFile(3D-mrc)
+ [-2[D] Out2D (NULL )] :Optional :OutputDataFile(2D-mrc projection(y-z))
+ [-d[elta] delta (5 )] :Optional :delta[A](mrc-file)
+ [-p[delphi] delphi (165 )] :Essential :deltaPhi
+ [-dp[delphi] deldelphi (5 )] :Optional :deltaDeltaPhi
+ [-z[deltaz] delz (5 )] :Essential :deltaz
+ [-n[Molecule] nMolecule (1 )] :Essential :NumberOfMolecules
+ [-nx nx (1 )] :Optional :Pixel[Def:]
+ [-ny ny (1 )] :Optional :Pixel[Def:]
+ [-nz nz (1 )] :Optional :Pixel[Def:]
+ [-Sx[tart] Startx (0.0 )] :Optional :Startx[A]
+ [-Sy[tart] Starty (0.0 )] :Optional :Starty[A]
+ [-Sz[tart] Startz (0.0 )] :Optional :Startz[A]
+ [-w[eight] Weight (1.0 )] :Optional :Weight
+ [-dx dx (2.5 )] :Optional :dx
+ [-dy dy (2.5 )] :Optional :dy
+ [-dz dz (2.5 )] :Optional :dz
+ [-startn startn (0 )] :Optional :start molecule's index
+ [-startC startID (A )] :Optional :start chain ID
+ [-deltaSeq deltaSeq (1000 )] :Optional :start chain ID
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbMove: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbMove</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbMove</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbMove
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-x X (0.0 )] :Optional :Move X[A]
+ [-y Y (0.0 )] :Optional :Move Y[A]
+ [-z Z (0.0 )] :Optional :Move Z[A]
+ [-originTo toX (0.0 )toY (0.0 )toZ (0.0 )] :Optional :move (0,0,0) to (X,Y,Z)
+ [-toOrigin fromX (0.0 )fromY (0.0 )fromZ (0.0 )] :Optional :move (X,Y,Z) to (0,0,0)
+ [-GCtoOrigin ] :Optional :GC(Gravity Centre) to origin
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbPCA: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbPCA</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbPCA</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbPCA
+ Options:
+ [-i[nput] In (stdin )] :Optional :InputDataFile
+ [-o[utput] Out (stdout )] :Optional :Output: Result
+ [-o[utput]U[nit] OutUnit (NULL )] :Optional :Output: Unit Vector Array
+ [-o[utput]M[atrix3D] OutMat3D (NULL )] :Optional :Output: Matrix3D from Unit Vector Array
+ [-o[utput]PDB OutPDB (NULL )] :Optional :Output: PDB rotated from Unit Vector Array
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbRhoFit: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbRhoFit</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbRhoFit</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbRhoFit
+ Options:
+ [-i[nput]pdb[File] InPdb (NULL )] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMrc (NULL )] :Essential :InputDataFile
+ [-o[utput of ]mrc OutMrc (NULL )] :Essential :OutputDataFile
+ [-o[utput of ]txt OutTxt (NULL )] :Optional :OutputDataFile
+ [-o[utput of ]par OutPar (stdout )] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL )] :Optional :OutputDataFile
+ [-xmin xmin (0 )] :Optional :xmin for fitting
+ [-xmax xmax (0 )] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 )] :Optional :delta x for fitting
+ [-ymin ymin (0 )] :Optional :ymin for fitting
+ [-ymax ymax (0 )] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 )] :Optional :delta y for fitting
+ [-zmin zmin (0 )] :Optional :zmin for fitting
+ [-zmax zmax (82 )] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 )] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS )] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 )] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 )] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 )] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 )] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 )] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 )] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 )] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 )] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 )] :Optional :delta theta for fitting(degree)
+ [-n[ormalize]w[eight]normalizeWeight (100000000.0)] :Optional :weight for normalize
+ [-n[ormalize]C[ontour]normalizeContour (0.0 )] :Optional :Contour Level for Normalize
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Zminus ] :Optional :Shift to -z
+ [-Tfactor ] :Optional :Consider T factor
+ [-T[ factor ]lim[it] Tlim (60 )] :Optional :The atom will be neglected
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ [-C[ontour] contourLevel (0.0 )... ] :Variable :ContourLevel
+
+
+ Usage of pdbRhoFit:
+ -ipdb : Filename of pdb file of atomic model
+ -imrc : Filename of mrc file of contour map
+ -omrc : Filename of mrc file of fitting results
+ -otxt : Filename of text file of fitting results
+ -opar : Filename of text file of fitting results
+ -opdb : Filename of pdb file with a max score after fitting results
+ -zmin : Initial value of z (should <= zmax)
+ -zmax : Final value of z
+ -zd : Delta z for fitting (should >0)
+ -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phimax : Final value of phi (should >0)
+ -phid : Delta phi for fitting (should >0)
+ -C : Contour level (variable and MUST be last option)
+ -Inverse: Protein has high density on the image
+ -Zminus : Atomic model shift to -z while fitting
+ -Tfactor: Consider temperature factor
+ -Tlim : The atoms whose T factor is above Tlim will be neglected
+ -Centre : Filament-axis is x=0, y=0
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+ 1 : Add the densities of atoms.
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbRhoFitTm: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbRhoFitTm</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbRhoFitTm</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbRhoFitTm
+ Options:
+ [-i[nput]pdb[File] InPdb (NULL )] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMrc (NULL )] :Essential :InputDataFile
+ [-o[utput of ]mrc OutMrc (NULL )] :Essential :OutputDataFile
+ [-Sx Sx (50 )] :Essential :x of rotation axis
+ [-Sy Sy (110 )] :Essential :y of rotation axis
+ [-Sz Sz (110 )] :Essential :z of rotation axis
+ [-o[utput of ]txt OutTxt (NULL )] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL )] :Optional :OutputDataFile
+ [-xmin xmin (0 )] :Optional :xmin for fitting
+ [-xmax xmax (0 )] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 )] :Optional :delta x for fitting
+ [-ymin ymin (0 )] :Optional :ymin for fitting
+ [-ymax ymax (0 )] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 )] :Optional :delta y for fitting
+ [-zmin zmin (0 )] :Optional :zmin for fitting
+ [-zmax zmax (82 )] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 )] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS )] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 )] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 )] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 )] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 )] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 )] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 )] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 )] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 )] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 )] :Optional :delta theta for fitting(degree)
+ [-n[ormalize]w[eight]normalizeWeight (100000000.0)] :Optional :weight for normalize
+ [-n[ormalize]C[ontour]normalizeContour (0.0 )] :Optional :Contour Level for Normalize
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Zminus ] :Optional :Shift to -z
+ [-Tfactor ] :Optional :Consider T factor
+ [-T[ factor ]lim[it] Tlim (60 )] :Optional :The atom will be neglected
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ [-C[ontour] contourLevel (0.0 )... ] :Variable :ContourLevel
+
+
+ Usage of pdbRhoFitTm:
+ -ipdb : Filename of pdb file of atomic model
+ -imrc : Filename of mrc file of contour map
+ -omrc : Filename of mrc file of fitting results
+ -otxt : Filename of text file of fitting results
+ -opdb : Filename of pdb file with a max score after fitting results
+ -zmin : Initial value of z (should <= zmax)
+ -zmax : Final value of z
+ -zd : Delta z for fitting (should >0)
+ -phimin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phimax : Final value of phi (should >0)
+ -phid : Delta phi for fitting (should >0)
+ -C : Contour level (variable and MUST be last option)
+ -Inverse: Protein has high density on the image
+ -Sx : x of rotation axis
+ -Sy : y of rotation axis
+ -Sz : z of rotation axis
+ -Zminus : Atomic model shift to -z while fitting
+ -Tfactor: Consider temperature factor
+ -Tlim : The atoms whose T factor is above Tlim will be neglected
+ -Centre : Filament-axis is x=0, y=0
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+ 1 : Add the densities of atoms.
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbShapeFit: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbShapeFit</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbShapeFit</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbShapeFit
+ Options:
+ [-i[nput]pdb[File] InPDB (NULL )] :Essential :InputDataFile
+ [-i[nput]mrc[File] InMRC (NULL )] :Essential :InputDataFile
+ [-C[ontour] Contour (0.0 )] :Essential :Contour
+ [-C[ontour]M[ode] ContourMode (0 )] :Optional :ContourMode: refer to mrcImageContourSurfaceCreate
+ [-o[utput of ]mrc OutMRC (NULL )] :Optional :OutputDataFile
+ [-o[utput of ]txt OutTxt (stdout )] :Optional :OutputDataFile
+ [-o[utput of ]pdb OutPDB (NULL )] :Optional :OutputDataFile
+ [-xmin xmin (0 )] :Optional :xmin for fitting
+ [-xmax xmax (0 )] :Optional :xmax for fitting
+ [-xd[elta] xDelta (1 )] :Optional :delta x for fitting
+ [-ymin ymin (0 )] :Optional :ymin for fitting
+ [-ymax ymax (0 )] :Optional :ymax for fitting
+ [-yd[elta] yDelta (1 )] :Optional :delta y for fitting
+ [-zmin zmin (0 )] :Optional :zmin for fitting
+ [-zmax zmax (82 )] :Optional :zmax for fitting
+ [-zd[elta] zDelta (1 )] :Optional :delta z for fitting
+ [-E[uler]A[ngle] EulerAngle (ZOYS )] :Optional :Euler Angle for three-angle
+ [-phimin phimin (0 )] :Optional :phimin for fitting(degree)
+ [-phimax phimax (194 )] :Optional :phimax for fitting(degree)
+ [-phid[elta] phiDelta (2 )] :Optional :delta phi for fitting(degree)
+ [-psimin psimin (0 )] :Optional :psimin for fitting(degree)
+ [-psimax psimax (0 )] :Optional :psimax for fitting(degree)
+ [-psid[elta] psiDelta (2 )] :Optional :delta psi for fitting(degree)
+ [-thetamin thetamin (0 )] :Optional :thetamin for fitting(degree)
+ [-thetamax thetamax (0 )] :Optional :thetamax for fitting(degree)
+ [-thetad[elta] thetaDelta (2 )] :Optional :delta theta for fitting(degree)
+ [-P[DB]C[ontour]M[ode]surfaceMode (0 )] :Optional :PDB SurfaceMode: refer to pdbSurface
+ [-order order (1.7 )] :Optional :order: refer to pdbSurface
+ [-refine refine (2 )] :Optional :refine: refer to pdbSurface
+ [-size size (3 )] :Optional :size: refer to pdbSurface
+ [-weight weight (100 )] :Optional :weight: refer to pdbSurface
+ [-mergin mergin (3.0 )] :Optional :mergin: refer to pdbSurface
+ [-thres thresHold (0.0 )] :Optional :threshold: refer to pdbSurface
+ [-I[nverse] ] :Optional :Black is High Density.
+ [-Centre ] :Optional :Filament-axis is x=0, y=0
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ -ipdb : Filename : An atomic model to be fitted (PDB)
+ -imrc : Filename : 3-D density map (mrc-formated)
+ -omrc : Filename : fitting score map (MRC)
+ z=0: a max-score map of an phi-z plane which includes a max score point.
+ The max score mean a maximum score in all x-y-psi-theta plane with specific values of phi and z.
+ z=1: a max-score map of an psi-theta plane which includes a max score point.
+ The max score mean a maximum score in all x-y plane with specific values of psi, theta, phi and z.
+ z=2: a score map of an x-y plane which includes a max score point.
+ -otxt : Filename : fitting results (Text)
+ -opdb : Filename : An atomic model with a maximum score after fitting
+ -x|y|zmin : Initial value of z (should <= zmax)
+ -x|y|zmax : Final value of z
+ -x|y|zd : Delta z for fitting (should !=0)
+ -phi|psi|thetamin : Initial value of phi (should <= phimax; initial value of phi is 0)
+ -phi|psi|thetamax : Final value of phi (should !=0)
+ -phi|psi|thetad : Delta phi for fitting (should >0)
+ -C : Contour level of map file
+ -Inverse: Protein has high density on the image
+ -Centre : Filament-axis in an inPDBFile is along the line of x=0, y=0
+ -EA : Euler Angle Set : ZOYS: z -> y -> x
+ -c : Not used now
+ -m 0 : Count the atom number inside the contour.
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbTrans: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbTrans</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbTrans</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbTrans
+ Options:
+ [-i[nput] inFile (NULL ).as(inFile ) ] :Essential :Input: DataFile
+ [-o[utput] outFile (NULL ).as(outFile ) ] :Essential :Output: DataFile
+ [-M[atrix] matFile (NULL ).as(inFile ) ] :Optional :Input: MatrixFile[4][4]
+ [-E[uler]A[ngle] RotMode (YOYS ).as(String )
+ Rot1 (0.0 ).as(Real )
+ Rot2 (0.0 ).as(Real )
+ Rot3 (0.0 ).as(Real ) ] :Optional :Input:
+ [-cuda cudaDeviceID (0 ).as(Integer ) ] :Optional :cuda
+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
+ >>> Matrix3D File Format y = Ax + b<<<
+ a11 a21 a31 : Rotation Array : y=Ax
+ a12 a22 a32
+ a13 a23 a33
+ b1 b2 b3 : Translation Array : y = x + b
+ --- Attention ---
+ If both options of -M and -EA are set,
+ first, translation and rotation by -M will be performed
+ then, rotation by -EA will be done.
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: pdbTwoProteinFit: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>pdbTwoProteinFit</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>pdbTwoProteinFit</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: pdbTwoProteinFit
+ Options:
+ [-i[nput] In (NULL )] :Essential :InputDataFile
+ [-i[nput]res[idue] InResidue (NULL )] :Optional :ResidueInformationOfInputData
+ [-i[nput]sel[ectResidue]SelectIn (NULL )] :Optional :Output: Selected residue of in after fitting
+ [-r[ef] Ref (NULL )] :Essential :ReferenceDataFile
+ [-r[ef]res[idue] RefResidue (NULL )] :Optional :ResidueInfomationOfReferenceData
+ [-r[ef]sel[ectResidue]SelectRef (NULL )] :Optional :Output: Selected residue of after fitting
+ [-o[utput] Out (NULL )] :Essential :OutputDataFile
+ [-o[utput]Matrix Matrix (stdout )] :Optional :OutputMatrix
+ [-o[utput]Param Param (stdout )] :Optional :OutputParam
+ [-o[utput]Dis[tance] outDis (stdout )] :Optional :Output: PDB Distance as Temp
+ [-o[utput]Dis[tance]2outDis2 (stdout )] :Optional :Output: Distance List for Ca
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ >>>> Input and Reference File Format<<<<
+ ResidueNumberToBeFitted
+ ...
+ If |, all residules are sellected till the residue in the next line
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
++<<<<<<< HEAD
+/bin/bash: commonLinesSearchByVoting: そのようなファイルやディレクトリはありません
++=======
+ <HTML>
+ <HEAD>
+ <TITLE>commonLinesSearchByVoting</TITLE>
+ </HEAD>
+ <BODY>
+ <H1>commonLinesSearchByVoting</H1>
+ <H2>Usage</H2>
+ <PRE>
+ Usage: commonLinesSearchByVoting
+ Options:
+ [-i[nput] In (NULL )] :Optional :InputCorrelationMapList
+ [-i[nput]c[ommonLines]InC (NULL )] :Optional :InputCommonLinesList
+ [-i[nput]c[orrect]c[ommonLines]InCC (NULL )] :Optional :InputCorrectCommonLinesList
+ [-o[utput] Out (NULL )] :Essential :OutputFilteredCommonLinesList
+ [-o[utput]a[ll] OutA (NULL )] :Optional :OutputAllCommonLinesList
+ [-o[utput]d[etecting]r[ate]OutDR (NULL )] :Optional :OutputDetectingRate
+ [-o[utput]d[etecting]r[ate]a[ll]OutDRA (NULL )] :Optional :OutputDetectingRateALL
+ [-o[utput]p[eaks]h[istgram]OutPH (NULL )] :Optional :OutputPeaksHistgram
+ [-e[stimation]n[umber]en (1 )] :Optional :EstimationNumber
+ [-th[resholdLevel] th (1 )] :Optional :ThresholdLevel
+ [-histgramCreate[Flag]] :Optional :HistgramCreateFlag
+ [-extend[VotingFlag] ] :Optional :ExtendVotingFlag
+ [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
+ [-m[ode] mode (0 )] :Optional :Mode
+ ----- Additional Usage -----
+ Common lines are filtered only top G*100/sqrt(N) %, where N is the number of projections.
+ -extend Option
+ Execute extended voting.
+ -m Option
+ 0: normal
+ 1: self voting (each angle histgram peak is multiplyed by its correlation value)
+ -th Option
+ :
+ -1: G = 2^(-1)
+ 0: G = 2^0
+ 1: G = 2^1
+ 2: G = 2^2
+ :
+ -en Option
+ Estimation number of common line in a map.
+ Running time is proportional to this number.
+ Default; 1: the largest value in a correlation map is detected as common line.
+ MapList Format
+ numOfProjection1 numOfProjection2 mapFileName
+ : : :
+ CLinesList Format
+ numOfProjection1 numOfProjection2 [ degOfProjection1 degOfProjection2 degDiff cor ] mapFileName
+ : : : : : : :
+ Voting Algorithm by Amit Singer et al (2010),
+ "Detecting consistent common lines in cryo-EM by voting " (doi:10.1016/j.jsb.2009.11.003)
+ ----------------------------
+ </PRE>
+ </BODY>
+ </HTML>
++>>>>>>> FETCH_HEAD
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