[phenixbb] help with phenix.ligand_identification

Edward A. Berry BerryE at upstate.edu
Tue Sep 26 14:04:41 PDT 2017


Ligandfit itself has more helpful error message:
Sorry the string 'S2063' cannot be interpreted as a residue number?
(Duh!)
and does actually place the ligand in the requested blob with "search_center="
So I can run ligandfit in a foreach loop with each of the 180 ligands left by ligand_identification
=================

On 09/26/2017 03:32 PM, Edward A. Berry wrote:
> 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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