- phenixbb - phenix-online.org

Team Leader vacancy: PX group, SGC-Oxford
by Frank von Delft 01 Oct '07

01 Oct '07

I have a vacancy for Team Leader for Infrastructure and Methods Development in my group that is still being advertised; this is the Protein Crystallography group of the Structural Genomics Consortium, Oxford. For details, please see: http://www.sgc.ox.ac.uk/jobs/07079.html, and feel free to contact me if curious. The remit of the Structural Genomics Consortium (SGC) is to solve human proteins of medical relevance and place them in the public domain without restrictions; it is funded by a consortium of public and industrial funders, and has independently operating sites in Oxford and Toronto Universities and Karolinska Institutet (Stockholm). The Oxford site solved nearly 200 such structures in its first three years, and has now entered Phase II, with 4 years of funding till June 2011; it now has an increased emphasis on chemical biology and membrane proteins. The Protein Crystallography group collaborates tightly with the 5 other groups to get their purified proteins crystallized and solved -- five per month, to be precise. Equally importantly, with all the robotics and toys you'd care for, and access not only to lots of real-life samples but also to 3 years' worth of structured data accumulated during Phase I, we're ideally positioned for development and testing of crystallographic methods, which will be the major scientific thrust of the group in this phase. Enthusiastic crystallographers, especially those that really enjoy the nuts and bolts of the technique and mucking around with tricks and toys, both crystallization and algorithms, are encouraged to apply. Frank von Delft Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University, UK

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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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Problem in Autosol
by Eric Tee 15 Sep '07

15 Sep '07

Hi All, I was trying to run SAD phasing with phenix GUI for the first time. After conversion of mtz to sca file, at the step of autosol_scale_and_analyze_mad, I got the following message: failed to carry out Autosol_scale_and_analyze_mad None of the solve versions worked I'm pretty sure I choose the right package. Should I do something to configure solve? Eric

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elbow.builder to generate charges on individual atoms?
by Francis E Reyes 13 Sep '07

13 Sep '07

Ok, this is probably an unsupported feature(TM),but is there anyway to hack elbow.builder to output an electronic charge (presumably from the AM1 calculation) for each atom of a ligand? (by say substituting in for the Bfactor)) Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Position for PSI Knowledgebase development
by Paul Adams 12 Sep '07

12 Sep '07

======================================================================= Lawrence Berkeley National Laboratory Software Developer II ======================================================================= Software Developer II Job ID: 20930 Division: Physical Biosciences Date Opened: 8/7/2007 Summary This position will be part of the Computational Crystallography Initiative at Lawrence Berkeley Lab and will be responsible for developing a web site to disseminate information about the Technologies developed by the NIH Protein Structure Initiative (PSI). This program funds the majority of structural genomics efforts within the US and is responsible for the development of many new technologies that are useful to macromolecular crystallographers. This technology resource is part of the larger PSI Knowledge Base that will provide an information portal for the scientific community. Duties Essential: Under general direction of the Principal Investigator: Develop and maintain web site documenting PSI developed technologies. Interact with PSI researchers to collect information about new technologies. Create a relational database to store crystallographic data. Install and maintain SVN repositories for the PSI community. Marginal: Perform routine analysis of crystallographic data. Maintain web site computing hardware and software. Other duties as assigned. Qualifications Essential: Experience with writing and maintaining HTML web pages. Knowledge of standard programming methods, and Python in a UNIX environment. Strong analytical and organizational skills. Ability to handle multiple tasks in parallel. Excellent interpersonal skills for working in a diverse team environment, ability to interact effectively with other scientists, and to address their needs in an effective and timely manner. Marginal: B.S. Degree or higher in biophysics, computer science, chemistry, electrical engineering, physics or related field preferred or equivalent experience, with demonstrated programming experience. Experience maintaining computing hardware and software. Experience with analysis of crystallographic data. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20930. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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pseudo-merohedral twinning in P212121
by Schneider Sabine 12 Sep '07

12 Sep '07

Hi everyone, I have a data set to 2.8A, with most likely 2 molecules in the asu and a molecular replacement model with 40% sequence identity. (Cell 71.3 71.3 227.9 90 90 90) Initially the data appeared to be either P4322 or P43212 (Rsym = 7.4%; Cell 71.3 71.3 227.9 90 90 90), but the molecular replacement solutions had major clashes with the symmetry related molecules and a lower LLG for the solution of the second molecule. No twinning was detected by Xtriage. Processing the data in P212121 (Rsym 5.6%, cell 71.3 71.4 228.2 90 90 90) gave me a better molecular replacement solution (LLG 121/373), but I had 5 clashes with the second molecule in the asu. (I tested all alternative spacegroups) I also have a MAD dataset (very low quality!) and I combined the phases with the one obtained from molecular replacement in Sharp. After NCS averaging the maps had improved (still not great). I tried to improve things in the model and run Phaser again and the solution had better statistics (LLG 338/1223) and the clashes were reduced to 2. Xtriage detected pseudo-merohedral twinning with a twin fraction of 43% with twin operator -k, -h, -l. So I tried refining the model with phenix telling it the twinning operator and fraction, but R/Rfree are stuck around 45%. I also tried simulated annealing but that gave even higher R/Rfree. Is there anything I can do, or is it a hopeless case? Thanks for your help in advance! Sabine This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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phenix.refine error
by Jianghai Zhu 12 Sep '07

12 Sep '07

Hi, I was trying the twinning refinement by phenix.refine and I got the following error messages during TLS refinement. Traceback (most recent call last): File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 81, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1244, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 866, in refinement_machine h_params = h_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ adp_refinement.py", line 175, in __init__ macro_cycle = macro_cycle) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/tls/tools.py", line 600, in __init__ fmodel.info().show_targets(text = prefix+" start model", out = out) AttributeError: 'info' object has no attribute 'show_targets' Could somebody help me? Thanks. Jianghai PS. the version is 2007_08_18_1856. +++++++++++++++++++++++++++++++ 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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What does mmtbx.twin_map_utils output?
by Francis E Reyes 11 Sep '07

11 Sep '07

Specifically I'm asking about the obs_and_calc.mtz file it produces. Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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So I think I have a twinning problem... ?
by Francis E Reyes 10 Sep '07

10 Sep '07

Hi all The short of the long is that phenix.xtriage on a C2 data set shows twinning with 3 twinning operators (-h,-k-l -k-h-l and k,h,-l). Pushing it through twin_utils, the soution k,h,-l gives an r/rfree of 0.30 and 0.3014 when the twin fraction is 0.352 . The question is where to go from here? I try to phenix.refine the same model in phenix.xtriage (except the mtz file is from the latest round of refinement of that model) and the R/Rfree on macro cycle =2 is 30 and 34 . Unfortunately, it doesn't seem to finish the refinement, I get a seg fault. In the def file for the refinement I set twinning = True and twin_law = k,h,-l . I tried to subject the same model and the .ref file to an autobuild passing in a .eff file for refinement specifying the twin_law, and again I get a segfault / crash when refining the input model. Please advise! --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Twinning in phenix.autobuild?
by Francis E Reyes 10 Sep '07

10 Sep '07

Hello all So I discovered from xtriage that my crystal is twinned. I have a pretty decent model that xtriage says has an r/rfree of 30/30 to a resolution of 2.6. I wanted to try a phenix.autobuild at 2.8A. I couldn't find a parameter flag for autobuild that turns on twinning. I already autobuilt this model once, and the xtriage log did find that the crystal was twinned, but twinning in refinement of the model during rebuilding wasn't turned on. Is there a way to tell autobuild to rebuild using twinning? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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crash during refinement with twinned data
by Scott White 10 Sep '07

10 Sep '07

Dear PhenixBB, I'm trying to refine a structure against potentially twinned data. I got the twin law from xtriage. phenix.refine starts, and at some point crashes with the messages below. Refinement proceeds to the end if I don't include twinning. Any suggestions? Thanks, Scott Traceback (most recent call last): File "/software/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/software/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 81, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/software/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1325, in run log = log) File "/software/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 559, in refinement_machine log = log) File "/software/phenix-1.3b/mmtbx/mmtbx/refinement/rigid_body.py", line 347, in __init__ fmodel_copy = fmodel.resolution_filter(d_min = res) File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py", line 1042, in resolution_filter sf_and_grads_accuracy_params = dc.sfg_params File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py", line 890, in __init__ u_part=self.scaling_parameters.u_part ) RuntimeError: cctbx Internal Error: /net/anaconda/scratch1/phenix/phenix-1.3b/cctbx/include/cctbx/xray/f_model.h(91): CCTBX_ASSERT((f_mask.size() == 0) || (hkl.size() == f_mask.size())) failure. -- _______________________________________ Dr Scott A. White Protein Crystallography Group School of Biosciences University of Birmingham B15 2TT E: s.a.white(a)bham.ac.uk T: +44-(0)121-414-7534 F: +44-(0)121-414-5925 W: http://www.bip.bham.ac.uk/cryst ______________________________________

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Re: [phenixbb] Unknown atoms revisitied
by Ralf W. Grosse-Kunstleve 07 Sep '07

07 Sep '07

> Does the atom type have to be a known element or can it something like > element X as seen in some pdb files? > > An example from 1aqn: > HETATM 1951 UNK UNX 277 -4.541 50.540 38.754 0.25 13.93 X > HETATM 1952 UNK UNX 278 -4.443 49.701 37.169 1.00 15.64 X Pavel is correct, but I'll add a some more details. If you want to use these atoms in refinement, you have to decide what scattering type to use. That has to be one of the symbols published in the International Tables for Crystallography, Volume C (see cctbx/eltbx/xray_scattering/it1992.cpp under $PHENIX or cci_app_sources). Regarding the .cif file: data_comp_SIN loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge SIN N N N 0.000 | | | | | this must be a valid "energy type" (see below) | this must be a valid scattering type symbol (Int. Tab.) this can be anything you want mon_lib/ener_lib.cif defines energy types (phenix.where_mon_lib_list_cif shows the path to mon_lib). You can define other energy types in additional .cif files you give to phenix.refine, using the same syntax as in the central ener_lib.cif. Regarding the .pdb file: HETATM 1952 UNK UNX 278 -4.443 49.701 37.169 1.00 15.64 X | | | | this must match the data_comp_UNX | | this must match _chem_comp_atom.type_symbol this must match _chem_comp_atom.atom_id You cannot use X in columns 77-78 because it must match _chem_comp_atom.type_symbol, and that in turn must be a valid scattering type symbol. However, you can leave the column blank. I think I'll change phenix.refine to treat the X like a blank, then you don't have to remove it. But in the current release you have no choice. Ralf

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Re: [phenixbb] Unknown atoms revisitied
by Ralf W. Grosse-Kunstleve 06 Sep '07

06 Sep '07

Hi Jeff, > I was wondering if there were any way to have a single unknown atom > recognized by phenix for refinement. Make up any residue name you like, e.g. SIN (for single N). Create a .cif file like this: data_comp_SIN loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge SIN N N N 0.000 In your PDB file add: ATOM 68 N SIN 15 20.000 20.000 20.000 1.00 20.00 N Add the name of the .cif file to the phenix.refine command line. You can have more than one data_comp_ in the same cif file, if you want to use different element types. Ralf

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Unknown atoms in refinement
by Jeff Habel 06 Sep '07

06 Sep '07

What's the best way of dealing with unknown atoms (UNK) in phenix.refine? I have a long disordered loop that runs basically the length of the protein on the back side and there is a single "amino acid" in the middle that I'm trying to model as UNK. I can run a round of refmac and auto generate a lib file with my ligand and the unk atoms but phenix.refine balks at that with respect to the Van der Waals radii. Thanks for the help, -Jeff

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wxu_scale during TLS + INDIVIDUAL_ADP refinement
by Jose M de Pereda 06 Sep '07

06 Sep '07

Dear colleagues, I am refining a structure with phenix.refine (cci_apps 2007_08_18_1856). The strategy includes refinement of tls, individual_adp, and individual_sites (during the same run.) In order to test different restraints for ADP´s refinement, I have changed the value of the wxu_scale from the default. Yet, the value of the wxu_scale parameter is always automatically reset to the same value as indicated in the log file under the section "Automatic adjustment due to TLS refinement". That is, phenix.refine uses in all cases the same wxu_scale independently of the value I set in the definitions file. Of course, when TLS refinement is not done, the wxu_scale value remains as specified. I would appreciate if someone could indicate me how to modify the ADPs restraints when doing TLS refinement. Cheers Jose -- -------------------------------------------------- Jose M de Pereda, PhD Centro de Investigación del Cáncer Spanish National Research Council - U. Salamanca Campus Unamuno s/n E-37007 Salamanca, Spain Phone: +34-923-294819 Fax: +34-923-294795 http://xtal.cicancer.org/ -------------------------------------------------

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statistics for highest shell in phenix.refine
by michael hothorn 05 Sep '07

05 Sep '07

Dear all, For the crystallographic table in my manuscript, can I define a highest shell in phenix.refine and have it output the refinement statistics for this range? If not, how can I calculate the highest shell statistics using the same parameters as used for the overall refinment? Thanks Michael

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