[phenixbb] help with phenix.ligand_identification

Edward A. Berry BerryE at upstate.edu
Tue Sep 26 12:32:44 PDT 2017


I'm having some problems using ligand_identification.
I would like to restrict the search to a specific density peak, even if it is not the highest unmodeled peak or the highest Fo-Fc peak in the map.
I tried using  options:
     search_center="67.5 18.3 11.8"
or
    ligand_near_res=S2063,
Will the search be restricted to that region, or if a particuar ligand doesn't fit that blob,
will it search through the rest of the map? If it is restricted, in what radius?
Is this radius affected by the "search_dist" or "local_search" parameters?
and local_search = True is default?
Is there a threshold level for density level, below which building a ligand in a blob will not be attempted?

I've tried with both search_center= and ligand_near_res=, and something gets
built far away from that site. But there were errors, so I may have something wrong:


phenix.ligand_identification mtz_in=sqr2803or13_031.mtz input_labels="2FOFCWT PH2FOFCWT" \
model=sqr2803or13_031.pdb ligand_near_res=S2063 nproc=2

After preparing the ligand library, then:
Running LigandFit process 1...

Number of atoms in ligand suc.pdb is 23
Running job sequence 1, ligand 2, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1...
Evaluating all ligands in ligand-lib now...and placing fittedligand ### in resolve_ligand_###.pdb

Number of atoms in ligand 2pe.pdb is 28
Running job sequence 0, ligand 1, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0...
Process Process-2:
Traceback (most recent call last):
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
     self.run()
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run
     self._target(*self._args, **self._kwargs)
   File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit
     shutil.rmtree(ligandfit_dir)
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree
     rmtree(fullname, ignore_errors, onerror)
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree
     onerror(os.rmdir, path, sys.exc_info())
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree
     os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1/LigandFit_run_1_/TEMP0'
Process Process-1:
Traceback (most recent call last):
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
     self.run()
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run
     self._target(*self._args, **self._kwargs)
   File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit
     shutil.rmtree(ligandfit_dir)
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree
     rmtree(fullname, ignore_errors, onerror)
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree
     onerror(os.rmdir, path, sys.exc_info())
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree
     os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0/LigandFit_run_1_/TEMP0'

Evaluating LigandFit results ...

The run continues, but it does not test any more ligands after those first two but goes on to evaluate the results.
With nproc = 1, only 1 ligand gets tested. In all cases the first ligand in the library (2PE.pdb) is evaluated as the best.
It is placed in density, but density that has already been built out with (and looks more like) a string of water molecules.
And this is far from the selected residue or coordinates specified.

The directory that raised the error when attempting to be deleted does eventually get removed: after the run there is no TEMP_N in the parent directory.

Any suggestions would be welcome.
Ed

P.S.
- running with .eff file:


['--show_defaults']
ligand_identification {
   mtz_in = sqr2803or13_031.mtz
   mtz_type = *F diffmap
   model = sqr2803or13_031.pdb
   ncpu = 1
   n_indiv_tries_min = 30
   n_indiv_tries_max = 300
   n_group_search = 4
   search_dist = 10
   local_search = True
   search_center = "67.5 18.3 11.8"
#  ligand_near_res = S2063
   verbose = False
   debug = False
   use_ligandfit = True
   search_mode = *default LigandFit
   temp_dir = Auto
   dry_run = False
#  number_of_ligands = 1
   cc_min = 0.75
   open_in_coot = False
   non_bonded = True
   keep_all_files = False
#  cif_def_file_list =
   real_space_target_weight = 10
#  job_title = None
   ligandfit {
     }
}

gives:

[['2pe.pdb', 'suc.pdb',  . . . 'upl.pdb']]

/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2

*******************************************************************************

Sorry, the protein model file None does not seem to exist?

*******************************************************************************


Running LigandFit process 0...

Process Process-1:
Traceback (most recent call last):
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
     self.run()
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run
     self._target(*self._args, **self._kwargs)
   File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1122, in RunLigandFit
     shutil.copyfile(mtz_in,data_local)
   File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 82, in copyfile
     with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: 'None'

Evaluating LigandFit results ...

Lig_seq Placed/total cc_all  cc  cc_adj   score   Code  HBscore

Cannot find overall_ligand_scores.log0.  This could mean that none of that (sub)set of ligand fitted well.



None of the ligand fit the difference desity well enough. Please try the following --
1) if you input a custom library, try to use the default library (no extra keywords needed), or
2) if you used the default library already, ususlly this means that the density is too small (> 6 atome or more is needed.)
Exiting ......



No good ligand found.




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