CTFCorrection/CTFCorrection2/Makefile.config

   1 #
   2 #       This is Makefile for CTF Correction Demo.
   3 #
   4
   5 #### Input extention ####
   6 # These extensions must all be different.
   7 INI_PDB_EXT=pdb
   8 FIL_PDB_EXT=filpdb
   9 FIL_MRC_EXT=filmrc
  10 INPUT_3D_EXT=3d
  11
  12 #### Suffixes rule ####
  13 .SUFFIXES: .$(INI_PDB_EXT) .$(INI_MRC_EXT) .$(FIL_PDB_EXT) .$(FIL_MRC_EXT) .$(INPUT_3D_EXT) .$(INPUT_2D_EXT) \
  14                         .$(CTF_2D_EXT) .$(FFT_2D_EXT) .$(CTF_INFO_EXT) .$(OUT_CTF_EXT) .tiff
  15
  16 #### INCLUDE ####
  17 -include ../CTFCorrection1/Makefile
  18 -include ../../TIPS/CreateGridImage/Makefile.config
  19 -include INPUT_2D_LIST
  20 -include CTF_2D_LIST
  21 -include FFT_2D_LIST
  22 -include CTF_INFO_LIST
  23
  24 #### Definition ####
  25
  26 ### For pdbHelix
  27 HELIX_DELTA_PHI=165
  28 HELIX_DELTA_Z=5
  29 HELIX_NUM_MOL=840
  30 HELIX_PIXEL_X=2000
  31 HELIX_PIXEL_Y=2000
  32 HELIX_PIXEL_Z=2000
  33 HELIX_START_X=-1000
  34 HELIX_START_Y=-1000
  35 HELIX_START_Z=-1000
  36 HELIX_LENGTH_X=1
  37 HELIX_LENGTH_Y=1
  38 HELIX_LENGTH_Z=1
  39
  40 ### For pdb2mrc2d(Projection Angle of Filament)
  41 PROJECTION_ANGLE_TYPE=YOYS
  42 PROJECTION_ANGLE_1=60
  43 PROJECTION_ANGLE_2=60
  44 PROJECTION_ANGLE_3=0
  45 PROJECTION_PIXEL_X=$(HELIX_PIXEL_Z)
  46 PROJECTION_PIXEL_Y=$(HELIX_PIXEL_Z)
  47 PROJECTION_START_X=`expr $(PROJECTION_PIXEL_X) / 10`
  48 PROJECTION_START_Y=-`expr $(PROJECTION_PIXEL_Y) / 4`
  49 #PROJECTION_START_X=0
  50 #PROJECTION_START_Y=0
  51
  52 ### For mrcImageNoiseAdd
  53 SNRATIO=1
  54
  55
  56 #### Rules of the list created ####
  57 $(CTF_2D_EXT):$(INPUT_2D_LIST:.$(INPUT_2D_EXT)=.$(CTF_2D_EXT))
  58
  59
  60 ##### Commands #####
  61 InitialCTFDataFromPDB::
  62         make $(INPUT).$(FIL_PDB_EXT);
  63         make $(INPUT).$(INPUT_2D_EXT);
  64
  65 InitialCTFDataFromMRC::
  66         cp $(INPUT).$(INI_MRC_EXT) $(INPUT).$(INPUT_2D_EXT);
  67
  68 InitialSiemensStar::
  69         mrcImageSiemensStar -o $(INPUT).$(INPUT_2D_EXT) -m 2 -Shape $(SSTAR_SHAPE);
  70
  71 ProcessForInput::
  72         make $(INPUT).$(CTF_2D_EXT);
  73         ln -s $(INPUT).$(CTF_2D_EXT) $(INPUT).mrc;
  74         mrc2tiff -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)_org.tiff;
  75         mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT)_i.tiff -I;
  76         mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT).tif;
  77
  78 ##### Commands(Input to Output) #####
  79 .$(INI_PDB_EXT).$(FIL_PDB_EXT):
  80         pdbHelix -i $*.$(INI_PDB_EXT) -o $*.$(FIL_PDB_EXT) -p $(HELIX_DELTA_PHI) -z $(HELIX_DELTA_Z) -n $(HELIX_NUM_MOL) \
  81                         -nx $(HELIX_PIXEL_X) -ny $(HELIX_PIXEL_Y) -nz $(HELIX_PIXEL_Z) \
  82                         -Sx $(HELIX_START_X) -Sy $(HELIX_START_Y) -Sz $(HELIX_START_Z) \
  83                         -dx $(HELIX_LENGTH_X) -dy $(HELIX_LENGTH_Y) -dz $(HELIX_LENGTH_Z)
  84
  85 .$(FIL_PDB_EXT).$(INPUT_3D_EXT):
  86         pdb2mrc -i $*.$(FIL_PDB_EXT) -o $*.$(INPUT_3D_EXT) -m 1
  87
  88 .$(FIL_PDB_EXT).$(INPUT_2D_EXT):
  89         pdb2mrc2d -i $*.$(FIL_PDB_EXT) -o $*.$(INPUT_2D_EXT)tmp -w 100 -sig 1 -Rot 1 1 \
  90                         -d $(HELIX_LENGTH_X) $(HELIX_LENGTH_Y) -n $(PROJECTION_PIXEL_X) $(PROJECTION_PIXEL_Y) -s $(PROJECTION_START_X) $(PROJECTION_START_Y) \
  91                         -startEA $(PROJECTION_ANGLE_TYPE) $(PROJECTION_ANGLE_1) $(PROJECTION_ANGLE_2) $(PROJECTION_ANGLE_3);
  92
  93         mrcImageNoiseAdd -i $*.$(INPUT_2D_EXT)tmp -o $*.$(INPUT_2D_EXT) -SN $(SNRATIO);
  94         rm $*.$(INPUT_2D_EXT)tmp
  95
  96 .$(INPUT_2D_EXT).$(CTF_2D_EXT):
  97         mrcImageCTFObservation -i $*.$(INPUT_2D_EXT) -o $*.$(CTF_2D_EXT)tmp -ctfMode $(CTF_MODE) \
  98                                                         -kV $(CTF_KV) -Cs $(CTF_CS) -df $(CTF_DEFOCUS) -Ain $(CTF_AIN);
  99         mrcImageNoiseAdd -i $(INPUT).$(CTF_2D_EXT)tmp -o $(INPUT).$(CTF_2D_EXT) -NS $(NSRATIO) -SD 1;
 100         rm $(INPUT).$(CTF_2D_EXT)tmp;
 101
 102 .$(OUT_CTF_EXT).tiff:
 103         mrc2tiff -i $*.$(OUT_CTF_EXT) -o $*_ctf.tiff
 104