September 2007 - phenixbb - phenix-online.org

Request for C shell script file for phenix.refine
by Partha Chakrabarti 01 Oct '07

01 Oct '07

Hi, I am wondering if one can have master scripts (C shell) for the macro cycle of phenix.refine that can be used from the command line. It is easier to comment out an option than having to type the whole thing.. has anybody tried it? Similar scripts exist for solve/resolve and phaser.. I should not say it, I am myself not adverse to using the GUI, it is just easier when the poor postdoc sits with the boss.. typically I face the question: where is the script file & where is the log file :)) Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

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unintellible font
by Michael Sawaya 30 Sep '07

30 Sep '07

Dear Phenixbb, My recent installation of Phenix completed successfully, but the font in the Phenix graphics window is replaced by little rectangles. So, I cannot read any of the menus. Does anyone know how to fix this problem? I just installed phenix-1.3b-d7-intel-linux-2.6 on our Linux machine 2.6.19-1.2911.fc6 i686 During installation, the following warning is reported : ... > (pango-querymodules:17819): Pango-WARNING **: Engine reported invalid > script value 56 > (pango-querymodules:17819): Pango-WARNING **: Engine reported invalid > script value 63 > (pango-querymodules:17819): Pango-WARNING **: Engine reported invalid > script value 64 > updating fonts/local.conf file > running mkfontdir > rebuilding font cache > fc-cache: symbol lookup error: fc-cache: undefined symbol: > FcConfigNormalizeFontDir > > generating index.theme file ... And I also get the following message when executing phenix > Shell variable RSH_PATH not set > Error reading Pango modules file > > (python:26803): Pango-WARNING **: pango_shape called with bad font, > expect ugly output > (python:26803): Pango-WARNING **: pango_font_get_glyph_extents called > with null font argument, expect ugly output > (python:26803): Pango-WARNING **: pango_font_get_metrics called with > null font argument, expect ugly output > (python:26803): Pango-WARNING **: _pango_cairo_font_install called > with bad font, expect ugly output > Thank you for any help you can give. Mike Sawaya

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Re: [phenixbb] phaser with certain spacegroups
by Tom Terwilliger 29 Sep '07

29 Sep '07

Hi Joe, Yes, you can run phaser with a selected subset of the possible spacegroups in the GUI. Here is how: 1. Start the AutoMR wizard as usual, and on the 2nd screen... A. say Yes to "Search all (selected) space groups with same point group" B. Under 'Choose variable to set' , select "all_plausible_sg_list" 2. Then hit CONTINUE and you will get a list of space groups. Edit out the ones you do not want with "Parameter group options" button. You're done. When you hit CONTINUE again the wizard will carry on with just the selected space groups. 3. If you want to make sure everything is ok, before you hit CONTINUE in step 2 after selecting the space groups you like, you can also select "Search Criteria" in NAVIGATE and then the 2nd screen will come up again with just the space groups you chose. All the best, Tom T At 12:31 PM 9/28/2007, Joe Batchelor wrote: >Hi, > >Can I run phaser through the phenix GUI using some, but not all, of >the possible spacegroups? > >Thanks, >Joe >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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phaser with certain spacegroups
by Joe Batchelor 28 Sep '07

28 Sep '07

Hi, Can I run phaser through the phenix GUI using some, but not all, of the possible spacegroups? Thanks, Joe

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Bulk solvent scaling problems
by seglynn 25 Sep '07

25 Sep '07

Dear all, I am using phenix.refine for the first time to refine a 4.5A structure solved by MR with individual sites (stretching things a bit, I know) and a grouped ADP per domain. Below are the R-factor per cycle stats: REMARK ------------------------------------------------------------------------ REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.6464 0.6186 7.101344e+00 7.091899e+00 REMARK 1_bss: 0.3955 0.4006 6.825652e+00 6.806242e+00 REMARK 1_xyz: 0.3200 0.3622 6.675328e+00 6.720706e+00 REMARK 1_adp: 0.3201 0.3622 6.674498e+00 6.719426e+00 REMARK 2_bss: 0.3539 0.3804 6.736883e+00 6.752128e+00 REMARK 2_xyz: 0.3067 0.3427 6.639056e+00 6.687071e+00 REMARK 2_adp: 0.3062 0.3423 6.638917e+00 6.687168e+00 REMARK 3_bss: 0.3357 0.3685 6.706475e+00 6.735398e+00 REMARK 3_xyz: 0.3082 0.3469 6.652536e+00 6.702364e+00 REMARK 3_adp: 0.3076 0.3468 6.652984e+00 6.703972e+00 REMARK 3_bss: 0.3286 0.3659 6.701854e+00 6.743421e+00 REMARK ------------------------------------------------------------------------ You can see that after the intial scaling, each cycle of bulk solvent scaling and anisotropy correction leads to an increase in R-factors of ~2%. Has anyone seen this behaviour before and maybe suggest a solution? Alternatively, is there a way I can turn off the final cycle of bulk solvent scaling before outputting the pdb and maps? Thanks in advance, Steve Glynn

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Oxygen atoms in phenix.refine
by Daniele de Sanctis 25 Sep '07

25 Sep '07

Dear all, i'm experiencing a weird problem with phenix.refine. After a phenix.refine run with a pdb file that doesn't contain the atoms N, CA, C, and O all together (with sidechains atoms between C and O) the O atoms are displaced from their position. Is this a know problem? Is there anyone that have suggestions how to re-edit the pdb file accordingly instead of doing cut-past for too many atoms? thanks daniele -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartado 127 2781-901 Oeiras Portugal

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phenix and ncs
by Jan Abendroth 23 Sep '07

23 Sep '07

Hi all, I could not quite find an answer in the on-line documentation: - How does phenix.refine use ncs restraints? Does it use xyz or torsion angle restraints? - Can one define the tightness of the ncs restraints? - Can one put different restraints on mainchain and sidechain atoms? Cheers Jan -- Jan Abendroth deCode Biostructures Seattle/Bainbridge Island, WA, USA work: JAbendroth(a)decode.is home: Jan.Abendroth(a)gmail.com

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elbow builder / phenix question
by Sudharsan Sridharan 20 Sep '07

20 Sep '07

Hi all, Is it ok to use the cif files generated by PRODRG server directly in phenix refine ? I fit a ligand molecule in density in Coot using this cif file. but after refinement in phenix using the same cif file the ligand coordinates does not look right. Then I created a new cif file using elbow.builder (with final geometry option) for the coordinates fit in Coot. But I see differences in the bond properties in the new cif file compared with the one from PRODRG server. e.g. please see below for parts of the cif generated in these two. could you please advice how to get the right cif file using the server or phenix and do the refinement. in a related question, is the command to use for building the cif in phenix phenix.elbow or elbow.builder. the former is given in http://www.phenix-online.org/new-site/documentation/elbow.htm but didn't work (i'm using 1.3 beta) and the latter does work (which is good !). Thanks, Sid. from prodrg: DRG OAB CAK deloc 1.250 0.020 DRG CAK OAD deloc 1.250 0.020 DRG CAK CAM single 1.530 0.025 DRG CAM CAA double 1.390 0.020 DRG CAM OAJ single 1.360 0.022 DRG OAJ CAO single 1.435 0.033 DRG CAO CAI single 1.390 0.020 DRG CAO CAP single 1.530 0.025 DRG CAI CAG double 1.390 0.020 DRG CAG CAH single 1.390 0.020 DRG CAH CAN double 1.390 0.020 DRG CAN CAL single 1.530 0.025 DRG CAN CAP single 1.530 0.025 DRG CAL OAE deloc 1.250 0.020 DRG CAL OAC deloc 1.250 0.020 DRG CAP OAF single 1.430 0.025 DRG OAF HAA single 1.000 0.027 DRG CAA 1HAA single 1.000 0.020 DRG CAA 2HAA single 1.000 0.020 DRG CAO 1HAO single 1.000 0.020 DRG CAI 1HAI single 1.000 0.020 DRG CAG 1HAG single 1.000 0.020 DRG CAH 1HAH single 1.000 0.020 DRG CAP 1HAP single 1.000 0.020 from elbow.builder: ISC OAB CAK double 1.23599 0.02 ISC CAK OAD single 1.23956 0.02 ISC CAK CAM single 1.51571 0.02 ISC CAM CAA single 1.38593 0.02 ISC CAM OAJ single 1.35985 0.02 ISC OAJ CAO double 1.45557 0.02 ISC CAO CAI aromatic 1.38350 0.02 ISC CAO CAP aromatic 1.53664 0.02 ISC CAI CAG aromatic 1.37763 0.02 ISC CAG CAH aromatic 1.37668 0.02 ISC CAH CAN aromatic 1.37587 0.02 ISC CAN CAL single 1.53109 0.02 ISC CAN CAP aromatic 1.52972 0.02 ISC CAL OAE double 1.22830 0.02 ISC CAL OAC single 1.23738 0.02 ISC CAP OAF double 1.41071 0.02 ISC 1HAD OAD single 1.08000 0.02 ISC 1HAM CAM single 1.08000 0.02 ISC 1HAA CAA single 1.08000 0.02 ISC 2HAA CAA single 1.08000 0.02 ISC 3HAA CAA single 1.08000 0.02 ISC 1HAH CAH single 1.08000 0.02 ISC 1HAC OAC single 1.08000 0.02

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wxu scale in phenix.refine
by Jan Abendroth 18 Sep '07

18 Sep '07

Hi all, in the final stages of refining a structure, I would like to optimize the restraint weights for geometry and B factors. It seems to work fine for geometry by defining " refinement.target_weights.wxc_scale=1.0". However, when the respective definition for B-factors does not seem to have an impact at all. I tried both: "refinement.target_weights.wxu_scale=2.0" in the parameter file or "wxu_scale=2.0" in the command line. The main reason why I try to fiddle around with the B-weights is that coot gives me a whole bunch of red bars in the Temperature factor variance analysis... I am using phenix 1.3d (downloaded past Sunday), mac-intel-osx, osx-10.4.10 Any ideas? Cheers Jan

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Re: [phenixbb] Problem in Autosol
by Eric Tee 16 Sep '07

16 Sep '07

Hi Tom, Many thanks for your reply. I was running phenix in my d_drive (a vfat partition) and got the error message. However, when I moved the mtz file to a directory under home directory (home/user/phenix-local), The program work without any problem. Let me explain how this work: I'm running phenix on fedora7 (a dual boot machine with Windows). I installed phenix under home/user/program/phenix (not /usr/local). I have a vfat partition (as d_drive) where I keep all my data and basically process everything there. I got the error message if I run phenix in the vfat partition but the program can be run successfully under the home directory /home/user/phenix-local). Following is what I got if I run phenix in the vfat partition (d_drive): WORKDIR: /mnt/d_drive/ccp4_data/SAD/phenix-localmachine Checking for KnownWizards: ['AutoSol', 'AutoBuild', 'ImportRawData'] application method: Null Getting inputs on first pass... SETTING UP INPUTS AutoSol Wizard Screen 1 of 4 AutoSol: Choose data files for dataset #1 A "dataset" is a group of data with a single set of heavy-atom sites You will be able to combine the results of all datasets later Note: Data files can be any format. If they are not all Scalepack premerged or all Scalepack unmerged then all will be converted to Scalepack premerged SUMMARY Input files dataset #1 Se_pk.mtz Creating new Data Storage /mnt/d_drive/ccp4_data/SAD/phenix-localmachine/PDS/AutoSol.1 sh: TEMP0/temporary.com: Permission denied Could be something related to permission problem but I have set permission to read/write/execute in vfat partition by adding the following line to /etc/fstab: /dev/sda6 /mnt/d_drive vfat users,uid=eric,gid=users,umask=0002,utf8=true 0 0 Any suggestion to enable running phenix in the vfat partition? Eric On 9/16/07, Tom Terwilliger <terwilliger(a)lanl.gov> wrote: > > Hi Eric, > > Can you possibly check to see that you have a recent version of phenix: > > phenix.version will do this. > > > Then if that is ok, I'm not sure what is causing the problem. This > message means that solve could not run with the data it got, but > usually an error message should come up earlier if there is a > problem. Have a look at LAST.LOG in your AutoSol directory and see > if it has any hints. Also look at AutoSol_run_1_.output and see the > end of this log file. > > If none of those work, if you can send me your input data file I can > see if there is a problem with it (all I would need is the first 100 > lines or so). > -Tom T > >

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