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Re: [phenixbb] Question about restraints in individualB-factor re finement
by Schubert, Carsten [PRDUS] 25 May '07

25 May '07

Thanks Pavel,Nigel: so it looks as if neither approach works and I would need to split the ligands into seperate PDB files for a truly independent B-factor refinement. Thanks for the hint about the non-bonded interactions. That was useful. Cheers Carsten -----Original Message----- From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]]On Behalf Of Pavel Afonine Sent: Friday, May 25, 2007 12:51 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Question about restraints in individualB-factor refinement Hi Carsten, for the refinement of b-factors there is no difference between two options. We use the sphere b-factors restraints which are calculated based on interatomic distances and the information about alternative conformations is not used at that point. However if you refine the coordinates, the difference is significant: if you refine it as two separate residues then they will "see" each other for non-bonded interactions term calculation and hence will be pushed apart. Please let me know if you still have questions! Pavel. Schubert, Carsten [PRDUS] wrote: Hi, I have a question about the handling of restraints in the individual B-factor refinement routine. What I'd like to do is to refine a ligand, which can be present in 2 or more different conformations/orientations in its binding site. I'd like to use B-factor refinement on the various instances of the ligand, which one is the most relevant one, assuming that the most relevant conformation/orientation is associated with the lowest B-factor (Validity of that assumption set aside ...) My question is now is there any difference in the restraints applied to the b-factors in the scenarios where A) the ligand is modeled as alternate conformations i.e. ATOM 2724 C01AINH I 1 27.808 26.376 23.301 0.50 27.77 I C ATOM 2733 C01BINH I 1 30.898 22.496 17.340 0.50 22.15 I C ... vs. scenario B) where the same ligand is modeled as 2 different residues ATOM 2724 C01 INH I 1 27.808 26.376 23.301 0.50 27.77 I C ATOM 2733 C01 INH I 2 30.898 22.496 17.340 0.50 22.15 I C .... Basically, what I am trying to achieve is to uncouple the B-factor refinement of each individual instance of the ligand from its other instance(s). Are there any hidden pitfalls between these 2 scenarios I should be aware of? Many thanks for any input. Cheers Carsten _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Question about restraints in individual B-factor refinement
by Schubert, Carsten [PRDUS] 25 May '07

25 May '07

Hi, I have a question about the handling of restraints in the individual B-factor refinement routine. What I'd like to do is to refine a ligand, which can be present in 2 or more different conformations/orientations in its binding site. I'd like to use B-factor refinement on the various instances of the ligand, which one is the most relevant one, assuming that the most relevant conformation/orientation is associated with the lowest B-factor (Validity of that assumption set aside ...) My question is now is there any difference in the restraints applied to the b-factors in the scenarios where A) the ligand is modeled as alternate conformations i.e. ATOM 2724 C01AINH I 1 27.808 26.376 23.301 0.50 27.77 I C ATOM 2733 C01BINH I 1 30.898 22.496 17.340 0.50 22.15 I C ... vs. scenario B) where the same ligand is modeled as 2 different residues ATOM 2724 C01 INH I 1 27.808 26.376 23.301 0.50 27.77 I C ATOM 2733 C01 INH I 2 30.898 22.496 17.340 0.50 22.15 I C .... Basically, what I am trying to achieve is to uncouple the B-factor refinement of each individual instance of the ligand from its other instance(s). Are there any hidden pitfalls between these 2 scenarios I should be aware of? Many thanks for any input. Cheers Carsten

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probable RTFM question
by William Scott 17 May '07

17 May '07

Howdie: I just used phenix.geometry_minimization to try to see the effect of deleting some disulphide bonds in a protein structure. Is there a way to do the equivalent of CNS's model_anneal (i.e., simulated annealing with just a model)? It wasn't apparent from reading the phenix.refine docs. Thanks. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/

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Re: [phenixbb] statistics output by phenix.refine
by Ralf W. Grosse-Kunstleve 17 May '07

17 May '07

> Are these maximum likelihood targets the normal maximum likelihood > function or the minus one? We are using the maximum likelihood targets described here: Lunin, V.Y., Afonine, P.V. & Urzhumtsev, A. (2002). Acta Cryst. A58, 270-282. Lunin, V.Y. & Skovoroda, T.P. (1995). Acta Cryst. A51, 880-887. > Should I expect an increase or decrease of the target? Decrease. But see below... > If the part of the restraints is not combined with > the x-ray part, the target is showing is not the actual target the > program is trying to maximize or minimize. Yes, that's right. > The values don't have a trend, at least I can't see a trend in my > log file. The x-ray target may go up since we refine x-ray target + geometry target. The total will always go down (that's how the minimizer works), but an individual contribution may go up a bit. Ralf

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statistics output by phenix.refine
by Jianghai Zhu 16 May '07

16 May '07

Hi, At the end of the log file output by phenix.refine, only R and Rfree are output. Is it possible to generate a statistical table which includes R, Rfree, FOM, LLG (total), LLG (free), rmsd (bond), rmsd (angle), ... for every refinement cycle? I want to monitor the progress of my refinement. Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Using Phenix to calculate Atom Maps
by James Fraser 14 May '07

14 May '07

Hello, Is there a way to use Phenix to calculate maps that are just representative of the model? This would be similar to the ATMMAP mode of SFALL or using model_fcalc.inp/model_phase.inp in CNS. Thanks, James

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Reflection output
by Rife, Christopher L 09 May '07

09 May '07

Hi, In trying to get a reflection file written out after refinement with phenix.refine (version 2007_03_13_2155), we found a couple of problems. 1. The documentation gives the example of including "export_final_f_model=mtz" in the command line input, however, phenix complains that it does not know this command. It is possible to work around this by changing "write_refined_fmodel_to_file" in the param file to true. 2. When the model is refined with twinning, trying to write out the reflection file causes it to crash with the following error: > Writing refined fmodel to plain text file: > /data5/Completed/PH10062D-47717/Phenix/model_001_fmodel.hkl > Traceback (most recent call last): > File > "/home/sdcsoftware/linux/cci_apps_sources/phenix/phenix/comman > d_line/refine.py", line 5, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/home/sdcsoftware/linux/cci_apps_sources/phenix/phenix/refine > ment/command_line.py", line 86, in run > if(output.write_refined_fmodel_to_file): > refine_object.write_refined_fmodel(f_hkl) > File > "/home/sdcsoftware/linux/cci_apps_sources/phenix/phenix/refine > ment/driver.py", line 927, in write_refined_fmodel > self.fmodel.dump(out = f) > AttributeError: 'twin_model_manager' object has no attribute 'dump' We are trying to prepare files for deposition, so any assistance would be welcome. Thanks, Chris ----------------------------------------- Structure Determination Core Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory

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Remodelling using Phenix
by Ethayathulla A.S 04 May '07

04 May '07

hi I am doing structure at 2.3A resolution. It is a dimer not NCS. I have probelm in tracing last 10 amino acids in the C-terminus in both chains. Both chains come close each other and winds up. So Iam finding difficulty in tracing the chain. I used phenix for rebuilding with all the amino acid included. But autorebuilding is not rebuilding properly, whatever input is given it rebuilds on that. Actually it should be a helix and only at lower cuff off we can observe density for main chain so I tried phenix rebuild to improve it but it's not working. Is there any option to use phenix. I used rebuilding with option automatic and input coordinates and sequence. plz suggest do improve the phases. -- A.S.Ethayathulla Department of BIophysics All India Institute of Medical Sciences Ansai Nagar New Delhi-110029 India

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Re: [phenixbb] PHENIX user mailing list <[email protected]>
by Ralf W. Grosse-Kunstleve 16 Apr '07

16 Apr '07

Hi James, > Number of atoms with unknown nonbonded energy type symbols: 14 > "CD CD D 1 " > "CD CD D 2 " This problem should be fixed in the latest phenix development release (1.26 beta @ http://www.phenix-online.org/download/index.html) and the slightly more recent CCI Apps (link at same web page). Are you using phenix.refine from an older release? Could you please try the latest phenix or CCI Apps? Ralf

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Interpreting Cd atoms
by James Fraser 16 Apr '07

16 Apr '07

Hello, I'm trying to refine a structure with Cadmium bound. Is there a standard way to define "energy type symbols"? Thanks, James Number of atoms with unknown nonbonded energy type symbols: 14 "CD CD D 1 " "CD CD D 2 " "CD CD D 3 " "CD CD D 4 " "CD CD D 5 " "CD CD D 6 " "CD CD D 7 " "CD CD D 8 " "CD CD D 9 " "CD CD D 10 " ... (remaining 4 not shown) Time building chain proxies: 2.36, per 1000 atoms: 1.27 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 14 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions. Note that elbow.builder is available to create restraint definitions.

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