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Does phenix have any utility to do the 2mFo-DFc composite omit map calculations?
by zhangh1＠umbc.edu 03 Nov '10

03 Nov '10

Hi, Does phenix have any utility to do the 2mFo-DFc composite omit map calculations (similar to OMIT in CCP4)? Thanks in advance! Hailiang

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phenix.model_vs_data : resolution cutoff from .pdb
by Bryan Lepore 02 Nov '10

02 Nov '10

[ phenix dev-568 ] TIL using phenix.model_vs_data, if the "REMARK 3" records in .pdb are adjusted e.g. to set a resolution limit, e.g REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : [change to whatever high resolution limit] REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.511 phenix.model_vs_data will pick this up and compute the R-factors for that range. Thanks Pavel -bryan

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Riding H
by Jianghai Zhu 01 Nov '10

01 Nov '10

Hi all, If I use the riding H atoms come out of phenix.refine in molprobity, it gives me a decent clash score. But if I strip the H atoms and let molprobity to add H atoms, I get a much worse clash score. I saw the manual of phenix recommends the first method. So what is the cause of the difference here? I know long time ago that phenix and molprobity used different bond length to add the riding H atoms. I don't know what the situation is now. Does phenix.refine refine the riding H atom positions? Thanks. -- Jianghai

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cancel that ...
by Phoebe Rice 01 Nov '10

01 Nov '10

Despite the error messages, it really did make restraints that seem to work. I just didn't realize they'd be in a hidden directory. Can I put in a request for no hidden defaults? They make me feel like a trained monkey. thanks, Phoebe

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error in making links
by Phoebe Rice 01 Nov '10

01 Nov '10

Hi BB, I wanted to run phenix on a structure from the database with covalent serine-DNA links, 1zr4. The "ready-set" feature to prepare restraints from the pdb link records sounded lovely, but fails with the message "Error interpreting command line argument parament definition: "1ZR4.link.edits" RuntimeError: Unexpected end of input" This happens with either version 1.6.4-486 or a nightly build installed a few weeks ago (phenix 551; installed on 10/7/2010.) Am I asking to much to get nice Ser-DNA links without sweating blood to read the fine print? thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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refine : "merged" in .def
by Bryan Lepore 29 Oct '10

29 Oct '10

[ dev-564 on GNU/Linux ] why does phenix - apparently - keep putting the label "merged" in output .def's, when neither the input .def or .mtz has this label - and what generally is the significance? the .mtz has separate Bijvoets, and I's. e.g: input .def: (concise) labels = "I(+),SIGI(+),I(-),SIGI(-)" label = "R-free-flags" output .def: labels = "I(+),SIGI(+),I(-),SIGI(-),merged" label = "R-free-flags" i re-checked the .mtz lacks "merged" (not shown). -bryan

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Autobuild error - bash/dash/sh
by Stephen Graham 29 Oct '10

29 Oct '10

Hi there, Apologies if this has been reported before, but the autobuild job I tried to run last night failed after a short while... The job was started from the command line using: phenix.autobuild data=../mydata_free.mtz seq_file=../protein.fasta map_file=../ccp4i/protein_phaser.1_parrot2.mtz input_map_labels='parrot.F_phi.F parrot.F_phi.phi None' And it got to the point where it was trying to submit the three jobs before it died as follows: Splitting work into 3 jobs and running with 1 processors using sh background=False in /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0 Starting job 1...Log will be: /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.log *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'sh /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1' /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.sh: 5: Syntax error: Bad fd number ******************************************************************************** *************ERROR ENDING ******************* I think the problem might be that the RUN_FILE_1.sh script seems to use a bash command/redirection that is not implemented in plain old 'sh' spec, and thus not supported by dash (the lean version of sh that ships with ubuntu)? If I change the #! line of RUN_FILE_1.sh to call /bin/bash rather than /bin/sh the script seems to run to completion... Is there any easy way to change the script template to use /bin/bash or remove the offending command? I'm running phenix dev-550 on an x86 ubuntu 10.10 machine. Thanks, Stephen P.S. The reason I'm trying to run autobuild from the command line rather from the GUI is that the GUI seems to crash every time I give autobuild a sequence file in either the FASTA or PIR format. Is there another format I should be using? -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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Twin Law question
by Young-Jin Cho 28 Oct '10

28 Oct '10

Dear Phenix users, Thanks in advance to answer my question. As my recent data did not give me perfect statistics, I was wondering what the problem was (one of things is ice ring though). When I ran Xtriage with my struggling current data set and looked like I got twinned data. I reran PHASER as was suggested and confirmed that current space group is right. My question is now how I can handle this problem. First, as was recommended I input twin_law, however not all the cases (I have a couple of data sets) were working. One favorite(!) error message was as following: "Map type 'Fc' not supported for twinned structures. Allowed types: Fo-Fc, Fobs-Fobs-Fmodel, 2mFo-DFc, 2mFobs-DFmodel, mFo-DFc, mFobs-DFmodel, gradient, m_gradient." I got this from both GUI and shell environment. . 1. Now from now on, whenever I want to phenix.refine, should I include twin_law command such as 'twin_law=-h,l,k'? 2. In this case, what do I expect to see such as lowering Rfree or else? If it doesn't help lowering Rfree, what to do next? 3. Do I have to report I did with twinlaw option in case of preparing a paper or presentation? I mean I also heard that if one got twinned data, they re-collected data. How much can I convince my refinement is OK with twined data? Additionally, I checked other data, and applied twin_law but the result R/Rfree were exactly same as the one I refined without twin_law option, it this normal case? With many thanks in advance, Young-Jin Cho

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maximum allowable B-factor value
by Christian Roth 27 Oct '10

27 Oct '10

Dear all, I did a refinement run with a built in ligand. Within the ligand the B-factor jumps between two connected atoms from 60 up ~110, which is i think a bit too much. Is there a way to restrain the B-factors that they could not jump so much. I would accept negative difference density for the atom. Maybe the ligand is a bit degraded. Best regards Christian @Pavel Tanks for your suggestions with occupancy refinement and B-factors. -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

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Re: [phenixbb] Sigma-A vs Resolution plot
by Bryan Lepore 25 Oct '10

25 Oct '10

On Thu, Oct 21, 2010 at 12:04 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > the plot "Sigma-A vs Resolution" will be available in the next PHENIX > nightly build: Looks nice - I greatly appreciate this - thanks Pavel, Nat, anyone else I forgot. -Bryan

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