updated to also include truncate to create Fs and cut data resolution
This commit is contained in:
Beale John Henry
@@ -5,6 +5,7 @@
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"""
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# aim
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to make an mtz from an hkl file output from partialator or process_hkl
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runs f2mtz and then truncate for create an mtz with other intensities and structure factors
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# usage to make mtz from manually entered lengths and angles
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python make_mtz.py -i <path to .hkl file from partialator>
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@@ -14,6 +15,8 @@ python make_mtz.py -i <path to .hkl file from partialator>
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-d dataset name in mtz
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-g spacegroup
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-c list of cell lengths and angles to use - 59.3,59.3,153.1,90.0,90.0,90.0
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-r number of residues
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-A resolution range - e.g. 40.0,2.0
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# usage to make mtz from the mean angles and lengths in stream file
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python make_mtz.py -i <path to .hkl file from partialator>
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@@ -22,6 +25,8 @@ python make_mtz.py -i <path to .hkl file from partialator>
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-x xtal name in mtz
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-d dataset name in mtz
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-g spacegroup
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-r number of residues
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-A resolution range - e.g. 40.0,2.0
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-s <path to stream file>
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-u True
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@@ -29,8 +34,11 @@ python make_mtz.py -i <path to .hkl file from partialator>
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python make_mtz.py -s <path to stream file>
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# output
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- .mtz file
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- .html log file
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- .mtz file - just intensities
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- f2mtz.log file
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- _F.mtz file - intensities and structure factors
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- cuts data to desired resolution
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- truncate.log file
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"""
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# modules
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@@ -72,27 +80,49 @@ def get_mean_cell( stream_file ):
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return mean_cell, len(cell_lst)
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def make_mtz( hklout_file, mtzout_file, project, crystal, dataset, cell, spacegroup ):
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def make_mtz( hklout_file, mtzout_file, project, crystal, dataset, cell, spacegroup, residues, res_range ):
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# make_mtz file name
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mtz_run_file = "make_mtz.sh"
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# make F file name
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Fout_file = os.path.splitext( mtzout_file )[0] + "_F.mtz"
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# write file
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mtz_sh = open( mtz_run_file, "w" )
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mtz_sh.write( "#!/bin/sh\n\n" )
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mtz_sh.write( "module purge\n" )
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mtz_sh.write( "module load ccp4/8.0\n\n" )
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mtz_sh.write( "f2mtz HKLIN {0} HKLOUT {1} > out.html << EOF\n".format( hklout_file, mtzout_file ) )
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mtz_sh.write( "f2mtz HKLIN {0} HKLOUT {1} << EOF_hkl > f2mtz.log\n".format( hklout_file, mtzout_file ) )
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mtz_sh.write( "TITLE Reflections from CrystFEL\n" )
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mtz_sh.write( "NAME PROJECT {0} CRYSTAL {1} DATASET {2}\n".format( project, crystal, dataset ) )
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mtz_sh.write( "CELL {0} {1} {2} {3} {4} {5}\n".format( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5] ) )
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mtz_sh.write( "SYMM {0}\n".format( spacegroup ) )
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mtz_sh.write( "SKIP 3\n" )
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mtz_sh.write( "LABOUT H K L IMEAN SIGIMEAN\n" )
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mtz_sh.write( "CTYPE H H H J Q\n" )
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mtz_sh.write( "LABOUT H K L I_stream SIGI_stream\n" )
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mtz_sh.write( "CTYPE H H H J Q\n" )
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mtz_sh.write( "FORMAT '(3(F4.0,1X),F10.2,10X,F10.2)'\n" )
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mtz_sh.write( "SKIP 3\n" )
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mtz_sh.write( "EOF" )
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mtz_sh.write( "EOF_hkl\n\n\n" )
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mtz_sh.write( "echo 'done'\n" )
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mtz_sh.write( "echo 'I and SIGI from CrystFEL stream saved as I_stream and SIGI_stream'\n" )
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mtz_sh.write( "echo 'I filename = {0}'\n\n\n".format( mtzout_file ) )
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mtz_sh.write( "echo 'running truncate'\n" )
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mtz_sh.write( "echo 'setting resolution range to {0}-{1}'\n".format( res_range[0], res_range[1] ) )
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mtz_sh.write( "echo 'assuming that there are {0}' in assymetric unit\n\n\n".format( residues ) )
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mtz_sh.write( "truncate HKLIN {0} HKLOUT {1} << EOF_F > truncate.log\n".format( mtzout_file, Fout_file ) )
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mtz_sh.write( "truncate YES\n" )
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mtz_sh.write( "anomalous NO\n" )
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mtz_sh.write( "nresidue {0}\n".format( residues ) )
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mtz_sh.write( "resolution {0} {1}\n".format( res_range[0], res_range[1] ) )
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mtz_sh.write( "plot OFF\n" )
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mtz_sh.write( "labin IMEAN=I_stream SIGIMEAN=SIGI_stream\n" )
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mtz_sh.write( "labout F=F_stream SIGF=SIGF_stream\n" )
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mtz_sh.write( "end\n" )
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mtz_sh.write( "EOF_F\n\n\n" )
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mtz_sh.write( "echo 'done'\n" )
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mtz_sh.write( "echo 'I_stream and SIGI_stream from f2mtz converted to F_stream and F_stream'\n" )
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mtz_sh.write( "echo 'F filename = {0} (contains both Is and Fs)'".format( Fout_file ) )
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mtz_sh.close()
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# make file executable
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@@ -118,7 +148,7 @@ def cut_hkl_file( hklin_file, hklout_file ):
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hklout.close()
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def main( hklin_file, hklout_file, mtzout, project, crystal, dataset, cell, spacegroup ):
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def main( hklin_file, hklout_file, mtzout, project, crystal, dataset, cell, spacegroup, residues, res_range ):
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# remove final lines from crystfel hkl out
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print( "removing final lines from crystfel hklin" )
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@@ -129,7 +159,7 @@ def main( hklin_file, hklout_file, mtzout, project, crystal, dataset, cell, spac
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print( "making mtz" )
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print( "using cell constants\n{0} {1} {2} A {3} {4} {5} deg".format( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5] ) )
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print( "Titles in mtz will be:\nPROJECT {0} CRYSTAL {1} DATASET {2}".format( project, crystal, dataset ) )
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make_mtz( hklout_file, mtzout, project, crystal, dataset, cell, spacegroup )
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make_mtz( hklout_file, mtzout, project, crystal, dataset, cell, spacegroup, residues, res_range )
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print( "done" )
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def list_of_floats(arg):
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@@ -182,6 +212,18 @@ if __name__ == "__main__":
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help="list of complete cell length and angles, e.g. 59.3,59.3,153.1,90.0,90.0,90.0. They all should be floats",
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type=list_of_floats
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)
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parser.add_argument(
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"-r",
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"--residues",
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help="number of residues for truncate, e.g., hewl = 129",
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type=int
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)
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parser.add_argument(
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"-A",
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"--resolution_range",
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help="list of 2 floats - low res then high res cut off, e.g., 50.0,1.3",
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type=list_of_floats
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)
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parser.add_argument(
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"-s",
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"--stream_file",
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@@ -200,7 +242,7 @@ if __name__ == "__main__":
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if args.stream_file:
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print( "reading stream file" )
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cell, xtals = get_mean_cell( args.stream_file )
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print( "found {0} xtats".format( xtals ) )
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print( "found {0} xtals".format( xtals ) )
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print( "mean lengths = {0}, {1}, {2} A".format( cell[0], cell[1], cell[2] ) )
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print( "mean angles = {0}, {1}, {2} deg".format( cell[3], cell[4], cell[5] ) )
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print( "# for input to make_mtz = {0},{1},{2},{3},{4},{5}".format( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5] ) )
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@@ -210,11 +252,11 @@ if __name__ == "__main__":
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mtzout = args.mtzout
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else:
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mtzout = os.path.splitext( args.hklin )[0] + ".mtz"
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main( args.hklin, hklout_file, mtzout, args.project, args.crystal, args.dataset, cell, args.spacegroup )
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main( args.hklin, hklout_file, mtzout, args.project, args.crystal, args.dataset, cell, args.spacegroup, args.residues, args.resolution_range )
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if args.stream_file == None and args.use_stream == False:
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hklout_file = os.path.splitext( args.hklin )[0] + "_cut.hkl"
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if args.mtzout:
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mtzout = args.mtzout
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else:
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mtzout = os.path.splitext( args.hklin )[0] + ".mtz"
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main( args.hklin, hklout_file, mtzout, args.project, args.crystal, args.dataset, args.cell, args.spacegroup )
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main( args.hklin, hklout_file, mtzout, args.project, args.crystal, args.dataset, args.cell, args.spacegroup, args.residues, args.resolution_range )
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