[phenixbb] help with phenix.ligand_identification

Li-Wei Hung lwhung at lbl.gov
Wed Sep 27 21:47:05 PDT 2017


Hi Ed,

Sorry for  problems in ligand_identification.  The default is to use 
LigandFit processes (slower, but more thorough), so the search center 
syntax will be under ligandfit.search_target.search_center.  You can on 
the other hand use the faster ligand_id process with 
use_ligandfit=False, the your search_center should work.  I noticed that 
you are using map coefficients so mtz_type=diffmap should be set.  I 
short, you can either

phenix.ligand_identification mtz_in=sqr2803or13_031.mtz 
input_labels="2FOFCWT PH2FOFCWT" mtz_type=diffmap\
model=sqr2803or13_031.pdb ligandfit.search_target.ligand_near_chain=S 
ligandfit.search_target.ligand_near_res=2063 nproc=2 ....
(the two ligandfit.search_targets.ligand_near_xxx, and be replaced by 
ligandfit.search_target.search_center="n.n n.n n.n")
or
phenix.ligand_identification mtz_in=sqr2803or13_031.mtz 
input_labels="2FOFCWT PH2FOFCWT" mtz_type=diffmap\
model=sqr2803or13_031.pdb use_ligandfit=false ligand_near_res="chain S 
and resid 2063" (or search_center="n.n n.n n.n" )nproc=2

If you have further problems or questions on ligand_identification, 
please do not hesitates to email me with input files (off list), and 
I'll help straighten problems.
In any event, I will update the documentation to add examples, and 
probably change one of the search_center keywords to make things clearer.

Best regards,

Li-Wei




Edward A. Berry wrote:
> 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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