December 2008 - phenixbb - phenix-online.org

Completeness issue by phenix
by Young-Jin Cho 15 Dec '08

15 Dec '08

Hi, I was happy for using phenix but am struggling with a strange result on completeness calculation. One typical data set I used kept showing low completeness, so I used the same mtz, and pdb file on Refmac: it turned out has more than 98% whereas phenix.refine gave me about 46% completeness. I have slightly lower value of R but higher Rfree from phenix calculation without adding H atoms. I don't know if this is a bug or a problem on my data set (hopefully not). thanks in advance, YoungJin

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phenix GUI takes longer time to comeup
by shivesh kumar 15 Dec '08

15 Dec '08

Dear all The GUI of phenix installed in Fedora 8 takes longer time, sometimes 30mins. Can anyone help in this regard, what is the problem and how it can be sorted out? Thanx in advance Shivesh

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Re: [phenixbb] individual anisotropic adps
by Pavel Afonine 13 Dec '08

13 Dec '08

Currently phenix.refine does not support refinement of individual anisotropic ADP and TLS for the same set of atoms (see my previous email). However, in phenix.refine you can refine TLS and individual anisotropic ADP for non-overlapping set of atoms. Pavel. On 12/11/2008 8:34 AM, gerwald jogl wrote: > Thanks, that's roughly what I thought. How about tls and individual > anisotropic together? same strategy, just observe Rfree?

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individual anisotropic adps
by gerwald jogl 11 Dec '08

11 Dec '08

Hi All, I was wondering if there is information/recommendations out there for the resolution required to refine individual anisotropic adps. I think the recommendation for shelx is at least 1.5 A resolution. In addition, is phenix set up and would it make sense to combine tls with individiual anisotropic adps? All comments welcome, Gerwald

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Keeping the same origin
by Mo Wong 11 Dec '08

11 Dec '08

Hi all, I would like to compare maps from different phasing runs, so it would make my life much easier if I could keep the same origin. I recall this could be done in solve/resolve, but can't seem to find it mentioned in the phenix documentation. Any suggestions? Thanks!

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resolution bins
by Daniele de Sanctis 10 Dec '08

10 Dec '08

Hi, I was wondering how phenix.refine decide the number of resolution bins in which it shows the refinement statistics (R-free, phase error...). In the case I'm working on it prints out only three resolution bins. Thanks d -- Daniele de Sanctis, PhD Macromolecular Crystallography Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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Question regarding phenix.elbow
by Young-Jin Cho 03 Dec '08

03 Dec '08

Hi I would like to know how I can add H atoms to my ligand, ADP in the protein complex. I was trying to add H atoms to one of my ligand, ADP. When I types "phenix.elbow --final-geometry=test10bcoot_h_refine_001.pdb --residue=ADP --output=model_h", it went on but failed with the following error message: Traceback (most recent call last): File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1201, in <module> run() File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1108, in run molecule = post_process(molecule, options) File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 577, in post_process options, File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager pre_opt)) File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB original_order=original_order, File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String self.AdjustHydrogenNames() File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 940, in AdjustHydrogenNames if test_name[3]==" ": test_name[3]="0" TypeError: 'str' object does not support item assignment FYI. ADP is names as ADP as a residue name in the pdb file but has different chain names. By the way, I should mention that I used phenix.reduce first for adding H atoms but it was not able to add sugar H's in ADP molecule albeit other residues were fine. Thanks in advance for your help. Best, YoungJin

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Bulk solvent
by csantiag＠cnb.csic.es 03 Dec '08

03 Dec '08

Hi all, I'm refining a protein and after running phenix.refine I always get a bulk solvent refinement cycle at the end of the process. Is there any way to get rid of the last step? ------------------------------------------------------------------------ REMARK stage angl bond chir dihe plan repu geom_target REMARK 0 : 1.007 0.027 0.237 18.975 0.004 4.107 2.7953e-01 REMARK 1_bss: 1.007 0.027 0.237 18.975 0.004 4.107 2.7953e-01 REMARK 1_xyz: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01 REMARK 1_adp: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01 REMARK 2_bss: 1.844 0.015 0.087 19.502 0.005 4.106 1.9824e-01 REMARK 2_xyz: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01 REMARK 2_adp: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01 REMARK 3_bss: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01 REMARK 3_xyz: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 REMARK 3_adp: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 REMARK 3_bss: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 REMARK ------------------------------------------------------------------------ César Santiago Dept of Macromolecules Structure Centro Nacional de Biotecnología, CSIC Campus Cantoblanco 28049 Madrid Spain csantiag(a)cnb.csic.es

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anomalous scatters refinement
by Daniele de Sanctis 02 Dec '08

02 Dec '08

Hi, I'm making some refinement tests with anomalous data and I wanted to try to refine the anomalous contribution. When would it be the best stage when to introduce it? Thanks D -- Daniele de Sanctis, PhD Macromolecular Crystallography Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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