Ejemplo n.º 1
0
 def create_coot_start_script(self,dir_for_scr,output_file_root):
     script_location = os.path.join(dir_for_scr ,"coot_start.sh")
     cootscr = open(script_location,"w")
     coot_str = """#!/bin/bash\n
     coot --auto {output_file_root}.2.mtz --pdb {output_file_root}.2.pdb""".format(output_file_root = output_file_root)
     print coot_str
     safe_write_script(coot_str,cootscr)
    def create_and_return_runscript_file(self):
        scrfile1 = open(os.path.join(self.outputdir,"%s_1.sh" % self.proj_name),"w")
        outfile_prefix  = os.path.join(self.outputdir,self.proj_name)
        # scrfile2 = open(os.path.join(self.outputdir,"%s_2.sh" % self.proj_name),"w")
        # scrfile3 = open(os.path.join(self.outputdir,"%s_3.sh" % self.proj_name),"w")
        # scrfile4 = open(os.path.join(self.outputdir,"%s_4.sh" % self.proj_name),"w")
    
      #  print "PROJ_NAME_OUTPREFIX set to ", outfile_prefix ,"DIRECTORY"
        
        scr1 =  """#!/bin/sh 
#set -e
# bug # 3192 - run-all examples produce harvest files - well to counteract
# this here set HARVESTHOME to somewhere in $CCP4_SCR

#HARVESTHOME=${self.outputdir}
#export HARVESTHOME

#   from /home/hari/official_ccp4/ccp4-6.1.3/examples/unix/runnable
#   SCALEPACK2MTZ
#
#  h k l I+ SigI+ I- SigI-   were extracted from aucn.na4
#  (acentric data only), and put into scalepack format. 
#  This is simply to illustrate the procedure for getting 
#  scalepack data into CCP4. I don't really know if it
#  is a good example.
#
#  (You can use the same procedure whether or not you have 
#  anomalous data.)
scalepack2mtz hklin {self.filename}  hklout {outfile_prefix}_junk1.mtz <<eof
name project {self.proj_name} crystal {self.proj_name} dataset {self.proj_name}
symm {self.spag}
end
eof

# convert Is to Fs and Ds.

truncate hklin {outfile_prefix}_junk1.mtz hklout {outfile_prefix}_junk2.mtz <<eof
title {self.proj_name} data 
truncate yes
nresidue {self.number_of_residues_in_asu}
labout  F=FP_{self.proj_name} SIGF=SIGFP_{self.proj_name}
end
eof

# get correct sort order and asymmetric unit

cad hklin1 {outfile_prefix}_junk2.mtz hklout {outfile_prefix}_trn.mtz <<eof
labi file 1 ALL
sort H K L
end
eof

# Add free r to reflections
freerflag hklin  {outfile_prefix}_trn.mtz hklout  {outfile_prefix}_trnfreeR.mtz <<eof
FREERFRAC 0.05
END
eof""".format(self=self, outfile_prefix = outfile_prefix)
        safe_write_script(scr1,scrfile1)
        return scrfile1.name
Ejemplo n.º 3
0
 def write_runscript_and_return_name(self):
     comfile = open(
         os.path.join(
             os.path.join(self.auriga_output_directory_root, self.proj_name), self.proj_name + "_phaser_input.sh"
         ),
         "w",
     )
     safe_write_script(self.mycomfile, comfile)
     return comfile.name
Ejemplo n.º 4
0
    def write_runscript_and_return_name(self):
        self.comstring = """#!/bin/csh
#
#   Example of refinement by refmac
#
set inmtz={self.outputdir}/{self.proj_name}_trnfreeR.mtz
start:

set name = {self.proj_name}
set last = 1
set cycles = 1
set count = 0
while ($count != $cycles)
echo '*******************************************************************'
echo  $count
echo '*******************************************************************'
@ curr = $last + 1

#
# Refmac 
#
refmac:
refmac5 \
HKLIN   $inmtz \
HKLOUT   {self.outputdir}/{self.proj_name}.${{curr}}.mtz \
XYZIN   {self.outputdir}/{self.proj_name}.${{last}}.pdb \
XYZOUT  {self.outputdir}/{self.proj_name}.${{curr}}.pdb \
<< eor
#
#####Do not add hydrogens
#
MAKE_restraints HYDRogens No
#
#####Do not check correctness of all monomers. Rely on users naming
#####One should be careful in using this option.
#
MAKE CHECk 0
#
####Input mtz labels. 
#
LABIN FP=FP_{self.proj_name} SIGFP=SIGFP_{self.proj_name} FREE=FreeR_flag
#
####Output mtz labels
#
LABO FC=FC PHIC=PHIC    FWT=2FOFCWT PHWT=PH2FOFCWT -
                     DELFWT=FOFCWT  PHDELWT=PHFOFCWT
#
####Restrained refinement. Reflections between 20 1.5Å resolution will be used
#
REFI TYPE RESTrained RESOLUTION  20 1.10
#
####Use maximum likelihood residual
####Use maximum likelihood residual
#
REFI RESI MLKF
#
####Refine isotropic B values.
# 
REFI BREF ISOTropic  
#
####Use 0.35 as weighting between X-ray and geometry
# 
WEIGHT AUTO
#
####Scaling parameters. Use BULK solvent based on Babinet's principle.
####NB: Unless otherwise SOLVENT NO given contribution of bulk solvent
####based on constant value will be used. 
#
SCALe TYPE BULK   
#
####Fix Babinet's bulk solvent B value to 200.0
#
SCALe LSSCale FIXBulk 200.0
#
####number of refinement cycles
#
NCYC 2
#
####Monitor only overall statistics
# 
MONI MEDIUM
end
eor
if ($status) exit
#
@ last++
@ count++
end
""".format(self=self)
        self.mycomfile = open(os.path.join(self.outputdir,self.proj_name + "_refmac5_input.sh"),"w")
        safe_write_script(self.comstring,self.mycomfile)
        return self.mycomfile.name