November 2011 - phenixbb - phenix-online.org

reference model restrain error
by Stephan Barden 23 Nov '11

23 Nov '11

Dear all, I'm facing a problem with a fresh (yesterday) installation of phenix 1.7.2-869 refining a structure with 6 molecules per ASU at 3.25 A and using a different reference structure with 1 mol/ASU at higher resolution. I wrote an additional parameter file to assign the reference model to each of the six molecules, which worked well with an older version of phenix. After the upgrade neither taking the additional parameter file, nor auto alignment worked for me. The error comming up is always: RuntimeError : Duplicate sequence number and insertion code. Traceback: File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", line 67, in __call__ call_back_handler=callback) File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line 75, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 209, in __init__ log=self.log) File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 145, in __init__ self.get_reference_dihedral_proxies() File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 611, in get_reference_dihedral_proxies log=self.log) File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 398, in process_reference_groups raise e Has anyone observed a similar problem? Are there any suggestions? Thanks, StephanB.

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solve/resolve problem
by dingding830106＠sina.com 22 Nov '11

22 Nov '11

Dear all when I use SOLVE to deal with the SAD data, it will stop with a error message: “STOP at /net/longnose/scratch2/phenix/phenix-1.7.2-869/solve_resolve/solve/solve_2.cpp(3133)” Can you tell me what happen? wding

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How to reduce clashscore value
by CelinaSocek 22 Nov '11

22 Nov '11

Hi all, I'm now using phenix to refine a small protein about 300 residues long. The resolution of my data is about 2.9 angstrom. Currently I got a refined model with good R-factors about 23/26, RMSD very reasonable and no Ramanchandran outliers. However, I found that the clashscore is extremely high: 63!! And rotamer outliers are also a lot: 8.5%. I wonder, what kind of stretagy I can use to reduce this? Thank you very much! best, Celina

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test_hhr
by Alexander Batyuk 21 Nov '11

21 Nov '11

Dear all, The phenix_regression.wizards.test_command_line_rosetta_quick_tests command hangs at the test_hhr step in phenix-dev-910 on Mac OS X 10.6.8. What could be the reason for that? What kind of log files should I post? The firewall allowed to fetch files from the net. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Re: [phenixbb] How to reduce clashscore value
by CelinaSocek 20 Nov '11

20 Nov '11

Thank you Nat! I will try to fix as many clashes as I can in coot, and hope that I can manage to reduce it to around 20. ;) Also thank other suggestions and discussions! best, Celina > > Which version are you using? We made some changes over the summer > that improve the geometry, especially the clashscore - these are > present in version 1.7.2. If you're still using an earlier version, > this might largely fix the problem. However, if there is > conformational strain in the model, it is difficult to fix severe > clashes without further rebuilding. You should inspect the clashes in > Coot (the Phenix GUI has shortcuts for this, but Coot alone also has > this capability) and fix as many as possible yourself. It is > recommended that you use explicit hydrogen atoms when doing this, > since the reason for clashes is often not obvious if only heavy atoms > are used. (You don't necessarily need to refine with heavy atoms > though - they're just an aid to visualizing clashes.) > > The rotamer problem may be related; there isn't much you can do with > these except fix them manually, but relieving some of the clashes may > help. The dihedral angle restraints simply aren't that strong, so in > areas of weak density it can be difficult to completely prevent > outliers. > > -Nat > > > ------------------------------ > >

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multiple ligand conformations
by Leonard Thomas 20 Nov '11

20 Nov '11

Hello All, One of the groups here has run into a problem in the refinement of their structure or more specifically a ligand bound to the structure. Through a series of other experiments they know that a photo reaction occurs to the compound when exposed to high flux as found at your everyday synchrotron source. The exposure changes the bonding such that there are two conformations with a bit in between obviously. They collected 360 degrees worth of data and if the data is split you can model the two conformations depending which half of the data you use. They are trying to refine with all of the data and modeling of the ligand into the two conformations. In refmac they can model this with no problem but in Phenix the ligand adopts a chemically wrong conformation, sort of a halfway point between the two chemically relevant conformations. They have used Phenix to do similar refinements on other structures but it appears either the last release or the latest release is causing problems. They have started out with everything from 50% occupancy to shifting it towards on one conformation or the other and the ligand always ends up in the chemically wrong position. Data is in the 1.4-1.5 ang. range. Ideas? Thanks in advance. Len Leonard Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 lmthomas(a)ou.edu http://barlywine.chem.ou.edu Office: (405)325-1126 Lab: (405)325-7571

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multiple ligand conformations
by Yuri 20 Nov '11

20 Nov '11

Hi, When you say "wrong postion", what does it mean? are the 2 ligands you are trying to refine being "pushed away" from each other? If that is the case first thing I would check is the ALTLOC comlumn of their pdb file entries. Make sure one is ALTLOC A and the other ALTLOC B. I have refined with ligands in four different positions before using phenix before and got satisfactory results... Hope this helps, -- Yuri Pompeu

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MR_ROSETTA
by Wei Shi 18 Nov '11

18 Nov '11

Hi all, I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using: phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222 \ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\ When I run the above script, it gives the following error message: child process stderr output: command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1' /bin/sh: qsub: not found Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running. But, it takes forever to run. My questions is: 1. Does anyone happen to know why it tells me “qsub: not found” when I include “group_run_command=qsub” in my script? 2. When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running. But it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much! Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1 Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log

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error: Duplicate selections
by Sebastiano Pasqualato 16 Nov '11

16 Nov '11

Hi all, sorry guys, this might be a silly one, but I can't see where I'm making the mistake. Whenever I turn on TLS refinement, I get this error message. And, as you can see, the Log file doesn't tell me much more. I have generated the TLS groups wit the 'TLS groups selection' tool in phenix. Any hint? Thanks in advance, ciao s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

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Scattering from riding hydrogens?
by Damian Ekiert 16 Nov '11

16 Nov '11

Hello, I have a question regarding two parameters and how they affect riding hydrogens. contribute_to_f_calc = True high_resolution_limit_to_include_scattering_from_h = 1.6 At lower resolution, setting contribute_to_f_calc = false is frequently helpful when using riding hydrogens and has been discussed before. But what is high_resolution_limit_to_include_scattering_from_h = 1.6 doing? If scattering from hydrogens is only included at higher than 1.6A resolution, it would seem like contribute_to_f_calc = True/False would not have any effect at say, 3.5A, but comparing identical refinement runs with contribute_to_f_calc = True or contribute_to_f_calc = False clearly gives different results. Can hydrogens contribute to Fcalc in a way aside from their scattering, or is their contribution accounted for independent of the position of the riding hydrogen (e.g., additional scattering term added to the associated heavy atom)? I think I am misunderstanding what these two parameters are doing and would appreciate some clarification. Thanks, Damian Ekiert

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