May 2007 - phenixbb - phenix-online.org

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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