[phenixbb] help with phenix.ligand_identification
Edward A. Berry
BerryE at upstate.edu
Thu Sep 28 07:44:40 PDT 2017
Thanks, Li-wei,
That makes sense, I'll try those suggestions.
Meanwhile the foreach loop is up to ligand 79 and found a few with CC > 0.75.
But it won't provide the analysis that ligand_identification will.
Ed
On 09/28/2017 12:47 AM, Li-Wei Hung wrote:
> 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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