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.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]