Updated freehand scripts May 2012

3D_spi_to_3D_mrc.b

@@ -0,0 +1,23 @@
+#!/bin/csh -f
+
+set file = $1
+
+setenv IMAGIC_BATCH 1
+echo "! "
+echo "! "
+echo "! ====================== "
+echo "! IMAGIC ACCUMULATE FILE "
+echo "! ====================== "
+echo "! "
+echo "! "
+echo "! IMAGIC program: em2em ------------------------------------------------"
+echo "! "
+/opt/qb3/imagic-070813/stand/em2em.e <<EOF
+SPI
+SINGLE_FILE
+MRC
+3
+$file
+${file:r}.mrc
+NO
+EOF

EMAN_to_FREALIGN_fromParam_freeHand.py

@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+
+from sys import *
+import os
+from optparse import OptionParser
+import glob
+import subprocess
+from os import system
+import sys
+import optparse 
+from EMAN2 import *
+
+def setupParserOptions():
+        parser = optparse.OptionParser()
+        parser.set_usage("%prog -p <parameter filek>")
+        parser.add_option("-p",dest="param",type="string",metavar="FILE",
+                help="EMAN2 parameter file")
+
+        options,args = parser.parse_args()
+
+        if len(args) > 1:
+                parser.error("Unknown commandline options: " +str(args))
+
+        if len(sys.argv) < 2:
+                parser.print_help()
+                sys.exit()
+
+        params={}
+        for i in parser.option_list:
+                if isinstance(i.dest,str):
+                        params[i.dest] = getattr(options,i.dest)
+        return params
+
+def Eman2Freali(az,alt,phi):
+
+    t1 = Transform({"type":"eman","az":az,"alt":alt,"phi":phi,"mirror":False})
+
+    #t_conv = Transform({"type":"eman","alt":31.717474411458415,"az":90,"phi":-90,"mirror":False})
+
+    #t2 = t1*t_conv.inverse()
+
+    d = t1.get_params("eman")
+
+    psi = d["phi"]+90
+
+    if psi >360:
+
+        psi = psi-360
+
+    theta= d["alt"]
+
+    phi = d["az"]-90
+
+    return psi,theta,phi
+
+def main(params):
+	parm=params['param']
+
+	f=open(parm,'r')
+	out = open("%s_freeHand"%(parm),'w')
+	count=1
+	count2=1
+	count=1
+	for line in f:
+
+		l = line.split()
+
+		parmPSI = float(l[0])
+		parmTHETA = float(l[1])
+		parmPHI = float(l[2])
+		sx =(float(l[3]))
+		sy =(float(l[4]))
+		model = float(l[5])
+
+		psi,theta,phi = Eman2Freali(parmPSI,parmTHETA,parmPHI)	
+
+		out.write("%s 	%s	%s	%s	%s	%s\n"%(psi,theta,phi,sx,sy,model))
+
+
+	f.close()
+	out.close()
+
+#Need this at the end for the parse commands
+if __name__ == "__main__":
+     params=setupParserOptions()
+     main(params)

ctftilt.py

@@ -7,13 +7,13 @@
 stack2 = 'stack01'		#stack name for tilted particles
 
 #Inputs
-shrink = 4			#Binning factor for final particle stack
-new = 64			#Box size for binned particles
+shrink = 2			#Binning factor for final particle stack
+new = 128			#Box size for binned particles
 scale = 4			#Binning factor used for micrograph from which the particles were picked
 
 #CTFTILT inputs
-parm3 = "2.2,120.0,0.2,99993,15,2\n" # !CS[mm],HT[kV],AmpCnst,XMAG,DStep[um]
-parm4 = "128,400.0,8.0,2000.0,30000.0,500.0,30,5\n" #!Box,ResMin[A],ResMax[A],dFMin[A],dFMax[A],FStep
+parm3 = "2.2,120.0,0.07,80000,12.03141,2\n" # !CS[mm],HT[kV],AmpCnst,XMAG,DStep[um]
+parm4 = "128,400.0,8.0,2000.0,35000.0,500.0,30,5\n" #!Box,ResMin[A],ResMax[A],dFMin[A],dFMax[A],FStep
 
 #############		Script		###############
 
@@ -25,7 +25,7 @@
 
 p1 = open(paramOUT1,'wa')
 p2 = open(paramOUT2,'wa')
-cmd = "/opt/qb3/frealign-9.02/bin/ctftilt.exe"
+cmd = "/users/glander/myami_latest/appion/bin/ctftilt64.exe"
 
 #syntax: grep(regexp_string,list_of_strings_to_search)
 def grep(string,list):
@@ -34,9 +34,13 @@ def grep(string,list):
 
 list = glob.glob('*en_00.mrc')
 
+micro  = 1
+particle1 = 1
+particle2 = 1
+
 for file in list: 
-	tmp1 = re.sub("_00_","_01_",file)
-       	tiltname = re.sub("en_00","en_01",tmp1) 
+        tmp1 = re.sub("_00_","_01_",file)
+        tiltname = re.sub("en_00","en_01",tmp1)       
        	#Check if both files exist
 	if os.path.isfile(file) & os.path.isfile(tiltname):
                	a = subprocess.Popen(cmd, -1, stdin=subprocess.PIPE,stdout=subprocess.PIPE, stderr=subprocess.PIPE)
@@ -52,7 +56,8 @@ def grep(string,list):
 
         	while i <= tot:
 
-			p1.write('%s		%s		%s		%s\n' %(out3[0],out3[1],out3[2],out3[4]))
+			p1.write('%s		%s		%s		%s	%s	%s\n' %(out3[0],out3[1],out3[2],out3[4],str(particle1),str(micro)))
+			particle1 = particle1 + 1
 			i = i + 1
 
 		cmd2 = 'batchboxer input=%s.mrc dbbox=%s.box scale=%s output=%s.img' %(fname,fname,scale,stack1)
@@ -71,20 +76,23 @@ def grep(string,list):
 
                 while i <= tot:
 
-                        p2.write('%s    	%s      	%s      	%s\n' %(out3[0],out3[1],out3[2],out3[4]))
+                        p2.write('%s    	%s      	%s      	%s	%s	%s\n' %(out3[0],out3[1],out3[2],out3[4],str(particle2),str(micro)))
+			particle2 = particle2 + 1
                         i = i + 1
 
                 cmd2 = 'batchboxer input=%s.mrc dbbox=%s.box scale=%s output=%s.img' %(fname,fname,scale,stack2)
                 subprocess.Popen(cmd2,shell=True).wait()
 
-cmd3 = 'proc2d %s.img %s_dc4.img meanshrink=%s' %(stack1,stack1,shrink)
+		micro = micro + 1
+
+cmd3 = 'proc2d %s.img %s_dc%01d.img meanshrink=%s' %(stack1,stack1,float(shrink),shrink)
 subprocess.Popen(cmd3,shell=True).wait()
 
-cmd4 = 'proc2d %s_dc4.img %s_dc4_%03d.img clip=%s edgenorm=0,1' %(stack1,stack1,float(new),new)
+cmd4 = 'proc2d %s_dc%01d.img %s_dc%01d_%03d.img clip=%s edgenorm=0,1' %(stack1,float(shrink),stack1,float(shrink),float(new),new)
 subprocess.Popen(cmd4,shell=True).wait()
 
-cmd3 = 'proc2d %s.img %s_dc4.img meanshrink=%s' %(stack2,stack2,shrink)
+cmd3 = 'proc2d %s.img %s_dc%01d.img meanshrink=%s' %(stack2,stack2,float(shrink),shrink)
 subprocess.Popen(cmd3,shell=True).wait()
 
-cmd4 = 'proc2d %s_dc4.img %s_dc4_%03d.img clip=%s edgenorm=0,1' %(stack2,stack2,float(new),new)
+cmd4 = 'proc2d %s_dc%01d.img %s_dc%01d_%03d.img clip=%s edgenorm=0,1' %(stack2,float(shrink),stack2,float(shrink),float(new),new)
 subprocess.Popen(cmd4,shell=True).wait()

ctftilt_ace2_weiner.py

@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+
+#Output filenames
+paramOUT1 = 'parameter_00.par'	#param filename for untilted particles
+paramOUT2 = 'parameter_01.par'	#param filename for tilted particles
+stack1 = 'stack00'		#stack name for untilted particles
+stack2 = 'stack01'		#stack name for tilted particles
+
+#Inputs
+shrink = 2			#Binning factor for final particle stack
+new = 256			#Box size for binned particles
+scale = 4			#Binning factor used for micrograph from which the particles were picked
+
+#CTFTILT inputs
+parm3 = "2.2,120.0,0.07,80000,12.03141,2\n" # !CS[mm],HT[kV],AmpCnst,XMAG,DStep[um]
+parm4 = "128,400.0,8.0,20000,30000,1000.0,30,5\n" #!Box,ResMin[A],ResMax[A],dFMin[A],dFMax[A],FStep
+
+#############		Script		###############
+
+from decimal import *
+import subprocess
+import sys
+import re
+import os
+import glob
+
+p1 = open(paramOUT1,'wa')
+p2 = open(paramOUT2,'wa')
+cmd = "/users/glander/myami_latest/appion/bin/ctftilt64.exe"
+
+#syntax: grep(regexp_string,list_of_strings_to_search)
+def grep(string,list):
+        expr = re.compile(string)
+        return filter(expr.search,list)
+
+list = glob.glob('*en_00.mrc')
+
+l = parm3.split(',')
+ang = Decimal(str(10**10))
+apix = str(((Decimal(l[4])*(Decimal(str(10**-6))))/Decimal(l[3]))*ang)
+cs = Decimal(l[0])/1000
+kv = l[1]
+
+for file in list: 
+	tmp1 = re.sub("_00_","_01_",file)
+       	tiltname = re.sub("en_00","en_01",tmp1) 
+       	#Check if both files exist
+	if os.path.isfile(file) & os.path.isfile(tiltname):
+               	a = subprocess.Popen(cmd, -1, stdin=subprocess.PIPE,stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+		[o,e] = a.communicate('%s\n'%(file) + '%s.diag\n'%(file) + parm3 + parm4)
+		out = grep("Final Values", o.split("\n"))
+		out2 = out[0]
+		out3 = out2.split()
+
+		fname = file.strip('.mrc')
+       		b = open('%s.box'%(fname))
+        	tot = len(b.readlines())
+        	i = 1
+
+        	while i <= tot:
+
+			p1.write('%s		%s		%s		%s\n' %(out3[0],out3[1],out3[2],out3[4]))
+			i = i + 1
+
+		#Weiner filter (with Ace2) micrograph before boxing
+
+		ang = Decimal(str(10**10))		
+
+		df1 = -1*(Decimal(out3[0])/ang)
+		df2 = -1*(Decimal(out3[1])/ang)
+		astig = (out3[2])
+
+		df = '%s,%s,%s' %(df1,df2,astig)	
+
+		cmd3 = '/users/glander/myami_latest/appion/bin/ace2correct.exe -img %s -kv %s -cs %s -apix %s -df %s -wiener 0.1' %(file,kv,cs,apix,df)
+		subprocess.Popen(cmd3,shell=True).wait()
+
+		cmd2 = 'batchboxer input=%s.mrc.corrected.mrc dbbox=%s.box scale=%s output=%s.img' %(fname,fname,scale,stack1)
+		subprocess.Popen(cmd2,shell=True).wait()
+
+		a = subprocess.Popen(cmd, -1, stdin=subprocess.PIPE,stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+                [o,e] = a.communicate('%s\n'%(tiltname) + '%s.diag\n'%(tiltname) + parm3 + parm4)
+                out = grep("Final Values", o.split("\n"))
+                out2 = out[0]
+                out3 = out2.split()
+
+                fname = tiltname.strip('.mrc')
+                b = open('%s.box'%(fname))
+                tot = len(b.readlines())
+                i = 1
+
+                while i <= tot:
+
+                        p2.write('%s    	%s      	%s      	%s\n' %(out3[0],out3[1],out3[2],out3[4]))
+                        i = i + 1
+
+                cmd2 = 'batchboxer input=%s.mrc dbbox=%s.box scale=%s output=%s.img' %(fname,fname,scale,stack2)
+                subprocess.Popen(cmd2,shell=True).wait()
+
+cmd3 = 'proc2d %s.img %s_dc%01d.img meanshrink=%s' %(stack1,stack1,float(shrink),shrink)
+subprocess.Popen(cmd3,shell=True).wait()
+
+cmd4 = 'proc2d %s_dc%01d.img %s_dc%01d_%03d.img clip=%s edgenorm=0,1' %(stack1,float(shrink),stack1,float(shrink),float(new),new)
+subprocess.Popen(cmd4,shell=True).wait()
+
+cmd3 = 'proc2d %s.img %s_dc%01d.img meanshrink=%s' %(stack2,stack2,float(shrink),shrink)
+subprocess.Popen(cmd3,shell=True).wait()
+
+cmd4 = 'proc2d %s_dc%01d.img %s_dc%01d_%03d.img clip=%s edgenorm=0,1' %(stack2,float(shrink),stack2,float(shrink),float(new),new)
+subprocess.Popen(cmd4,shell=True).wait()

e2proc3d.b

@@ -0,0 +1,24 @@
+#!/bin/csh -f
+
+set file = $1
+
+setenv IMAGIC_BATCH 1
+echo "! "
+echo "! "
+echo "! ====================== "
+echo "! IMAGIC ACCUMULATE FILE "
+echo "! ====================== "
+echo "! "
+echo "! "
+echo "! IMAGIC program: em2em ------------------------------------------------"
+echo "! "
+/opt/qb3/imagic-070813/stand/em2em.e <<EOF
+IMAGIC
+SPI
+SINGLE_FILE
+3
+${file:r}
+${file:r}.spi
+LINUX
+NO
+EOF

e2proc3d_all.b

@@ -0,0 +1,24 @@
+#!/bin/csh -f
+
+set file=$1
+
+setenv IMAGIC_BATCH 1
+echo "! "
+echo "! "
+echo "! ====================== "
+echo "! IMAGIC ACCUMULATE FILE "
+echo "! ====================== "
+echo "! "
+echo "! "
+echo "! IMAGIC program: em2em ------------------------------------------------"
+echo "! "
+/opt/qb3/imagic-110326/stand/em2em.e <<EOF
+IMAGIC
+SPI
+SIN
+3
+${file}
+${file}.spi
+LINUX
+YES
+EOF

e2proc3d_all.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python 
+
+#This will convert all volumes within an HDF file into separate SPIDER volumes
+
+#To run:
+
+#./e2proc3d_all.py volume_file.hdf [volume number wanted]
+
+import glob
+import subprocess
+import sys
+
+f = sys.argv[1]
+num=float(sys.argv[2])
+
+new=f.strip('.hdf')
+
+cmd="e2proc3d.py --first=%01d --last=%01d %s %s_%03d.hdf" %(num,num,f,new,num)
+subprocess.Popen(cmd,shell=True).wait()
+
+cmd="proc3d %s_%03d.hdf %s_%03d.img imagic" %(new,num,new,num)
+subprocess.Popen(cmd,shell=True).wait()
+
+cmd="/home/michael/BATCHLIB/freeHand/e2proc3d.b %s_%03d.img" %(new,num)
+subprocess.Popen(cmd,shell=True).wait()
+
+cmd="rm %s_%03d.hdf" %(new,num)
+subprocess.Popen(cmd,shell=True).wait()
+
+cmd="rm %s_%03d.hed %s_%03d.img" %(new,num,new,num)
+subprocess.Popen(cmd,shell=True).wait()
+
+cmd="~michael/BATCHLIB/freeHand/mirror_vols_spi.py %s_%03d.spi" %(new,num)
+subprocess.Popen(cmd,shell=True).wait()
+
+