[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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