- phenixbb - phenix-online.org

NAG-ASN link
by Jianghai Zhu 08 Oct '07

08 Oct '07

Hi, I got the following error when I added a NAG-ASN link in the def file. /nfs/home/jzhu/xiao/x61b/phenix6/temp/x61b.pdb Monomer Library directory: "/nfs/home/jzhu/phenix-1.3b-rc3/ext_ref_files/mon_lib" Total number of atoms: 46651 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain S and resname NAG and resid 1001 residue_selection_2: chain A and resname ASN and resid 15 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 46651 Number of chains: 8 Number of residues, atoms: 909, 13713 Unexpected atoms: {'ASN%DEL-HD22,HD22': 1} Classifications: {'peptide': 909} Modifications used: {'DEL-HD22': 1, 'NH3': 1} Link IDs: {'PTRANS': 59, 'TRANS': 847, 'PCIS': 2} Chain breaks: 3 Number of residues, atoms: 601, 8947 Classifications: {'peptide': 601} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 569, 'PCIS': 3} Chain breaks: 2 Number of residues, atoms: 898, 13559 Classifications: {'peptide': 898} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 59, 'TRANS': 836, 'PCIS': 2} Chain breaks: 3 Number of residues, atoms: 602, 8954 Classifications: {'peptide': 602} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 570, 'PCIS': 3} Chain breaks: 2 Number of residues, atoms: 642, 642 Classifications: {'water': 642} Link IDs: {None: 641} Number of residues, atoms: 31, 780 Unusual residues: {'MAN': 7, 'NAG%DEL-O1': 1, 'NAG': 23} Classifications: {'undetermined': 31} Modifications used: {'DEL-O1': 1} Link IDs: {None: 30, 'NAG-ASN': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen chiralities: 30 Number of residues, atoms: 16, 16 Unusual residues: {' MG': 2, ' CA': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Number of residues, atoms: 4, 40 Unusual residues: {'IMD': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Number of atoms with unknown nonbonded energy type symbols: 1 "HD22 ASN A 15 " Time building chain proxies: 32.54, per 1000 atoms: 0.70 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 1 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. Couldn't figure out what went wrong. Can somebody help me? 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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twin fraction
by Jianghai Zhu 06 Oct '07

06 Oct '07

Hi, I am using the phenix 1.3 beta rc3 to refine a twinned structure. In the old version, phenix.refine would report a twin fraction for each cycle of refinement. I could not find the twin fraction anymore in either the log file or the output pdb file. Where is it now? 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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Hinge movement for refine?
by Partha Chakrabarti 05 Oct '07

05 Oct '07

Hiya, I have used rigid body refinement in phenix.refine as suggested: refinement.refine.sites { rigid_body = chain A rigid_body = chain B } If I have a multidomain protein like kinases, or G proteins which have flexible switches, how can I define the region within a given chain? Best, 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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Re: [phenixbb] Question about strategy in phenix.refine
by Pavel Afonine 05 Oct '07

05 Oct '07

Hi, this figure from phenix.refine manual illustrates the refinement protocol the best (although it's a bit sketchy): http://phenix-online.org/documentation/refinement.htm#anch8 Pavel. > 2007/10/4, Partha Chakrabarti <ppchak(a)gmail.com>: > >> I am just trying to figure out certain details. For example, if one chooses >> multiple options in the strategies, how does the program decide if step 1 >> is nearly done and it can go to step 2? Of course I guess the whole process >> is iterative (macro cycle?) but having a bit control so to say.. >>

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Question about strategy in phenix.refine
by Partha Chakrabarti 04 Oct '07

04 Oct '07

Hiya, I am wondering what is the meaning of the * in the following: strategy = *individual_sites rigid_body *individual_adp group_adp tls \ individual_occupancies group_occupancies group_anomalous none Does it mean, that this option can be used (for example for high res) but not used as default? Maybe I missed it, how can i get the cif files for ligands? Refmac generates it in several cases, can that be used? Regards, 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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Team Leader vacancy: PX group, SGC-Oxford
by Frank von Delft 02 Oct '07

02 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 02 Oct '07

02 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 29 Sep '07

29 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 26 Sep '07

26 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 24 Sep '07

24 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 21 Sep '07

21 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 19 Sep '07

19 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 17 Sep '07

17 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 16 Sep '07

16 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 14 Sep '07

14 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 13 Sep '07

13 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 12 Sep '07

12 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 11 Sep '07

11 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 11 Sep '07

11 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 07 Sep '07

07 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 07 Sep '07

07 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 07 Sep '07

07 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 06 Sep '07

06 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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Re: [phenixbb] selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Thanks to all who replied. And thank you Ralf for your suggestion (quoted below), this worked very nicely! Somehow I missed this possibility in the online documentation. To reply to Pavel's question regarding how I figured out that tris is present at 1/2 occupancy: (1) density was first modelled with waters but they were too close together, and there was a fairly clear tetrahedral shape. (2) phosphate didn't refine well -- lead to huge negative difference peak at the P atom. (3) only other tetrahedral shape molecule in the soup was tris (TAM), and after refining just the tetrahedral core it was possible to see where the three arms extended. (4) b-factors for the tris were high relative surrounding protein atoms, and extraneous density suggested two alternate conformations for the nearby arg side-chain, one of which is too close to realistically exist next to the tris ligand. the other clue was that trial occupancy refinement of all atoms put most tris atoms in the 0.4-0.6 occupancy range. (5) tris with 0.5 occupancy, arg with two alt confs, plus a few waters at 0.5 occupancy is so far the best model with no significant different densities for this region. (6) the modelling will need to be confirmed with an SA omit ... > Hi Cathy, > > > The density suggests that when tris is not there, > > a side chain moves very close to that position > > You could model this with alternative conformations. If you assign > "altloc" A and B to two conformers of your protein, and just, say, B > to your TAM, then the ligand would only "see" your B protein. If you > don't define the B conformer (no atoms) then TAM wouldn't see that > part of the protein at all. > Actually, this approach seems better to me than working with > atom selections. > > Ralf

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Re: [phenixbb] selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Hi Ralf, That is disappointing. Lovely maps produced after a few phenix.refine runs for a 1.6 A structure revealed an unexpected tris ligand (TAM) with occupancy ~0.5. The density suggests that when tris is not there, a side chain moves very close to that position, thus my question. In other regards phenix seems a great step forward in automating refinement, and I look forward to new developments. best wishes, Cathy > Hi Cathy, > > > Is it possible to turn off nonbonded restraints for particular > > residues/monomers, or for atoms with occupancy less than 1.0? > > Nope, sorry. It is on the (long) to-do list. > BTW: each time someone asks the priority goes up. > > Ralf

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selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Hi Phenix bber's, I have been trying out phenix.refine and like it very much so far. Is it possible to turn off nonbonded restraints for particular residues/monomers, or for atoms with occupancy less than 1.0? Thanks, Cathy Lawson /////////////////////////////////////////////////////// http://rutchem.rutgers.edu/~lawson

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SAD related query
by tara kashav 05 Sep '07

05 Sep '07

Dear all, I am a novice user of phenix. I am trying to obtain phases for SAD dataset collected at 2.5 angs from autosol.But when i give the phases to autobuild, the R-factor is not decreasing below 49%. Also, in warp, it is unable to built with a message "encounterd an unknown element". Can someone suggest me what could be the problem. Thanks for any suggestion in advance. Tara Kashav On 9/3/07, phenixbb-request(a)phenix-online.org < phenixbb-request(a)phenix-online.org> wrote: > > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. command-line Patterson maps (Bryan W. Lepore) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 2 Sep 2007 00:07:51 -0500 (CDT) > From: "Bryan W. Lepore" <bryanlepore(a)mail.utexas.edu> > Subject: [phenixbb] command-line Patterson maps > To: phenixbb(a)phenix-online.org > Message-ID: > < > Pine.LNX.4.64.0709020001190.16588(a)cpe-70-116-17-26.austin.res.rr.com> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > will phenix calculate Pattersons from trial sites or a reflection file on > the command line? i.e. something besides hacking what is already there. > > e.g. cns has predict_patterson.inp. i can't seem to find a way to do it > from the command line - such as `phenix.patterson --sg=94 > reflections.mtz`. i saw phenix.maps but that looks like electron density > only. > > -bryan > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 22, Issue 1 > *************************************** > -- Tara Kashav, Dr. S. Gourinath's Lab, Lab No 430, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067

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command-line Patterson maps
by Bryan W. Lepore 04 Sep '07

04 Sep '07

will phenix calculate Pattersons from trial sites or a reflection file on the command line? i.e. something besides hacking what is already there. e.g. cns has predict_patterson.inp. i can't seem to find a way to do it from the command line - such as `phenix.patterson --sg=94 reflections.mtz`. i saw phenix.maps but that looks like electron density only. -bryan

2 1

ligand restraints
by Jeff Habel 31 Aug '07

31 Aug '07

I have a ligand with two phenyl rings where 2Fo and difference density clearly shows some torsion angle between the two rings. However, no matter how many times I tilt one ring refinement always makes them coplanar. Is there an option that I can use in phenix.refine to prevent the co-planarity or how do people typically handle this situation? Thanks for the help. All the best, -Jeff **************************************** Jeff Habel PhD Scripps Florida Drug Discovery 5353 Parkside Dr, RF-1 Rm 102 Jupiter, FL 33458 Phone: 561-799-8849 Fax: 561-799-8957 Email: jhabel(a)scripps.edu *****************************************

2 2

Turing off Auto-Modify initial isotropic ADP
by James Fraser 30 Aug '07

30 Aug '07

I'm trying to do an Fcalc with "main.number_of_macro_cycles=0 main.bulk_solvent_and_scale=false export_final_f_model=mtz ", but the b-factors get randomized before the 0th cycle of refinement (see excerpt from log below). Is there anyway to turn this off? Thanks, jf <<LOG FILE>> ----------Auto-Modify initial isotropic ADP---------- Randomizing |-ADP statistics (Wilson B = -4.823)------------------------------------------| .... -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

2 1

occupancy refinement question
by John Bruning 28 Aug '07

28 Aug '07

Hi, I have a ligand with dual conformations. I want to do group occupancy refinement on the conformers (each conformer is one group). I keep having trouble. The ligand is one chain named chain E and conformer 1 has residue name ADRG and conformer 2 has residue name BDRG. This is what I suppose my .def file should have in it: occupancies { individual = None group = "chain E and resname ADRG" group = "chain E and resname BDRG" one_occupancy_group_per_residue = True } When I run this it tells me I have an ambiguous selection. Any ideas why this isn't working and how I can change my .def file to make it work?

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Re: [phenixbb] occupancy refinement question
by Paul Adams 28 Aug '07

28 Aug '07

Hi is it possible that the A and B in the residue name are the alternate conformation ids? If so your selection should use the DRG resname and the altloc to select the appropriate residues. Paul Adams Lawrence Berkeley Laboratory -----Original Message----- From: John Bruning <jbruning(a)gmail.com> Date: Monday, Aug 27, 2007 1:38 pm Subject: [phenixbb] occupancy refinement question To: phenixbb(a)phenix-online.orgReply-to: PHENIX user mailing list <phenixbb(a)phenix-online.org> Hi, > >I have a ligand with dual conformations. I want to do group occupancy refinement on the conformers (each conformer is one group). I keep >having trouble. The ligand is one chain named chain E and conformer 1 has residue name ADRG and conformer 2 has residue name BDRG. This is what I suppose my .def file should have in it: > >occupancies { > individual = None > group = "chain E and resname ADRG" > group = "chain E and resname BDRG" > one_occupancy_group_per_residue = True > } > >When I run this it tells me I have an ambiguous selection. > >Any ideas why this isn't working and how I can change my .def file to make it work? >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb >

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PX Jobs Team Leader, Postdoc, Tech (SGC-Oxford).txt
by Frank von Delft 25 Aug '07

25 Aug '07

My group has several vacancies to fill immediately: a Team Leader for Infrastructure and Methods Development; two postdoc positions; and a technician. This is the Protein Crystallography group of the Structural Genomics Consortium, Oxford. For details, please see respectively: Team Leader: http://www.sgc.ox.ac.uk/jobs/07057.html Postdocs: http://www.sgc.ox.ac.uk/jobs/07058.html Technician: http://www.sgc.ox.ac.uk/jobs/07067.html Feel free to contact me for details. 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. As importantly, with all the robotics and toys you'd care for, and access not only to stacks of real, interesting samples but also to heaps 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. phx.

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Help making selections
by James Fraser 24 Aug '07

24 Aug '07

I am trying to refine a structure where I want chains C and D refined anisotropically. Chain A refined isotropically and as a TLS group. Chain B refined isotropically and as a (separate) TLS group. Chain S (waters) just refined isotropically. I've tried playing around with selections on the command line and in the .def file. Yet always end up not getting the refinement to run correctly or have phenix.refine throw an "AssertionError". I'm using the latest CCIapps phenix.refine. Can someone help me out. Below are the excerpt from the DEF file and the error message thrown to the screen. Thanks, James --FROM DEF FILE-- refine { strategy = *individual_sites rigid_body *individual_adp group_adp *tls \ individual_occupancies group_occupancies group_anomalous none sites { individual = None rigid_body = None } adp { individual { isotropic = None anisotropic = "chain c or chain d" } group = None one_adp_group_per_residue = True tls = "chain a" tls = "chain b" } occupancies { individual = None group = None one_occupancy_group_per_residue = False } anomalous_s --FROM LOG FILE-- ----------Target weights (before refinement)---------- Traceback (most recent call last): File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in ? command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 80, in run refine_object.run( File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1244, in run log = log) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 268, in refinement_machine log = log) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py", line 137, in __init__ compute_gradients = True) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/mmtbx/mmtbx/restraints.py", line 126, in energies_adp_aniso xray_structure = xray_structure, File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", line 113, in __init__ self.check_flags(fl_i) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", line 181, in check_flags assert not fl.use_u_aniso() AssertionError -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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Re: [phenixbb] density modification?
by Tom Terwilliger 23 Aug '07

23 Aug '07

Hi John, Yes, you have several choices for density modification in phenix: 1. Use your experimental Fobs and phases as a starting point for the AutoBuild Wizard. After the first cycle, you will have density-modified phases. In this example below model-building is turned off with maps_only=True to make this go quickly: phenix.autobuild my_fobs_exptl_phases.mtz input_seq_file=seq.dat \ maps_only=True \ n_cycle_build_max=1 n_cycle_rebuild_max=0 Your density-modified phases will be in AutoBuild_run_1_/overall_best_denmod_map_coeffs.mtz after this run. 2. You can also use resolve directly in phenix with a command like this phenix.resolve<<EOD hklin my_fobs_exptl_phases.mtz labin FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD no_build solvent_content 0.45 EOD Either of these will do solvent flattening and histogram matching. If you have ncs you can specify it with a set of matrices or with a set of heavy-atom positions in a PDB file that show the NCS with: ha_file heavy_atoms_with_ncs.pdb All the best, Tom T . 03:26 PM 8/22/2007, you wrote: >Is there a way to do density modification in Phenix (solvent and or >histogram)? If so how? > >Thanks, >John Bruning >_______________________________________________ >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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density modification?
by John Bruning 23 Aug '07

23 Aug '07

Is there a way to do density modification in Phenix (solvent and or histogram)? If so how? Thanks, John Bruning

2 1

Re: [phenixbb] Question about antibumping restraints and restraints on dihedrals
by Ralf W. Grosse-Kunstleve 22 Aug '07

22 Aug '07

Hi Madhu, > 1. Is there a way of applying antibumping restraints to decrease the > number of clashes in phenix.refine, I looked at older posts but couldn't > get a satisfactory guideline regarding the same. The antibumping restraints (nonbonded interactions) are on by default. Currently there isn't a syntax to turn them off or to change the default parameterization. If you refine for a few cycles with the weight for the x-ray target set to zero (wxc_scale=0) the clashes should definitely go away. Then go back to normal refinement (wxc_scale=0.5). I'd hope that the clashes don't come back. Otherwise that's what the x-ray data guide the minimization to, even though the restraints are pushing back. > 2. The default setttings for geometry refinement looks like this: > refinement.geometry_restraints.remove { > angles = None > dihedrals = None > chiralities = None > planarities = None > } > Do I have to change "dihedrals=True" This will not work: Sorry: Invalid atom selection: refinement.geometry_restraints.remove.dihedrals="True" (RuntimeError: Syntax error.) You have to specify atom selections to *remove* default restraints. > if I do not want to put restraints on > dihedrals. I was thinking that one puts restraints on psi/phi angles only > by setting "discard_psi_phi = False" because when I set it to > "discard_psi_phi = True", the Ramachandran plot was much better. But I did > not want to do this because then the Ramachandran plot is no more a > validation tool. I just wanted to know if Unknowingly I did that by > setting up "dihedrals = None". No, if you leave the geometry_restraints.remove block untouched you'll get all restraints incl. dihedrals, except for the peptide psi and phi angles, which are controlled by the dedicated parameter you quote. Cheers, Ralf

1 0

Question about antibumping restraints and restraints on dihedrals
by Madhumati Sevvana; Biotechnik 22 Aug '07

22 Aug '07

Hi! I could successfully refine a merohedral twin in phenix.refine but I have a few unanswered questions: 1. Is there a way of applying antibumping restraints to decrease the number of clashes in phenix.refine, I looked at older posts but couldn't get a satisfactory guideline regarding the same. 2. The default setttings for geometry refinement looks like this: refinement.geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } Do I have to change "dihedrals=True" if I do not want to put restraints on dihedrals. I was thinking that one puts restraints on psi/phi angles only by setting "discard_psi_phi = False" because when I set it to "discard_psi_phi = True", the Ramachandran plot was much better. But I did not want to do this because then the Ramachandran plot is no more a validation tool. I just wanted to know if Unknowingly I did that by setting up "dihedrals = None". Thank you in advance. Regards, Madhu. ------------------------------------------ Madhumati Sevvana, PhD Lehrstuhl fuer Biotechnik Friedrich-Alexander-Universitaet Henkestr. 91, D-91052 Erlangen, Germany Tel: 0049-9131-8523083 Email: msevvana(a)biologie.uni-erlangen.de -------------------------------------------

1 0

Re: [phenixbb] low res structures and Phenix
by Tom Terwilliger 21 Aug '07

21 Aug '07

Hi John, I'll answer the first of your questions... -Tom T >I have a couple of questions regarding low res structures in Phenix >(about 3.5 angstroms res). > >1. Can Phenix do B-factor sharpening for improved maps? If not >what program do people usually use for this? If you are using the AutoSol wizard, you can use the keywords: correct_aniso=True b_overall=20.0 to force correction of any anisotropy in your data and to set the overall B to 20.0. Note that this will affect all the maps produced by the AutoSol wizard. I have not yet found this to improve the quality of the resulting model; if it works for you please let me know! You can also use phenix.xtriage to do this: phenix.xtriage perfect.mtz hklout=output.mtz aniso.action=True aniso.final_b=user_b_iso aniso.b_iso=77 will set the b_iso of perfect.mtz to 77 >2. How can one optimize Ksol and Rprobe (bulk solvent model) in Phenix? > >3. Are there any other suggestions for dealing with low resolution >structures in Phenix? > >Thanks, >John Bruning >_______________________________________________ >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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cis peptide and pdb head
by Jianghai Zhu 21 Aug '07

21 Aug '07

Hi, How does phenix.refine treat cis peptide? Will it automatically detect it and restrain it like refmac5? or do I have to input the information somewhere? or generally how does phenix.refine treat the pdb head? I remember that some earlier version manual stated that all the head information are discarded, is that correct? 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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low res structures and Phenix
by John Bruning 21 Aug '07

21 Aug '07

Hi, I have a couple of questions regarding low res structures in Phenix (about 3.5 angstroms res). 1. Can Phenix do B-factor sharpening for improved maps? If not what program do people usually use for this? 2. How can one optimize Ksol and Rprobe (bulk solvent model) in Phenix? 3. Are there any other suggestions for dealing with low resolution structures in Phenix? Thanks, John Bruning

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Re: [phenixbb] autobuild wizard question
by Tom Terwilliger 20 Aug '07

20 Aug '07

Hi Jeff, I'm sorry for the trouble with the AutoBuild Wizard! I was not able to duplicate the problem with my version and putting in a model with 2 chains and trying to do rebuild_in_place of just a few residues, unfortunately. Everything seemed to work as it is supposed to. Can you check a couple things: 1. Make sure you have the latest version of PHENIX (development version) from the website. 2. Make sure that the range of residues you want to rebuild is at least 2 in from each end of the chain (so if the chain is 1-350, you can rebuild 3-6 or 347-348 but not 340-350). 3. If you accidentally give the Wizard a range that is too big, it should give you an error message and stop, but if you fix the range then it should go on. 4. Try running the Wizard from the command line, and specify "verbose=True debug=True" which will help because it gives you a lot of output that may help figure out what is going on. You will need to add also " |tee debug.log" to catch the output from this run. If none of those things help, then if you can send me the AutoBuild_run_xx_.output file from your GUI-version run and the output from running from the command line; that may help me figure out what is going wrong. Thanks! -Tom T Jeff Habel wrote: >Im a new PHENIX user and having trouble with the Autobuild wizard. > >The structure has 2 molecules in the asymmetric >unit and I am trying to build a small portion >(286-297) of both chains. I have tried building >both at the same time and trying just chain A >but always receive the error about needing 2 >amino acids on either end for anchoring the >build. Every time I alter the build range (284 >299 282 301 etc) the error persists. > >Any suggestions would be appreciated. > >Thanks, > >-Jeff 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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New CCI Apps
by Ralf W. Grosse-Kunstleve 20 Aug '07

20 Aug '07

On behalf of the Phenix development team I'm pleased to announce the release of a new CCI Apps version: http://phenix-online.org/download/cci_apps/ Send bug reports to: bugs(a)phenix-online.org For help write to: help(a)phenix-online.org Version 2007_08_18_1856 phenix.reduce updated to produce PDB-V3 hydrogen names (Duke group) phenix.refine updated to handle the new atom names from the remediated PDB-V3. Currently protein and RNA/DNA only. For ligands with new names, use elbow.builder to generate CIF files with matching restraints. phenix.refine manual significantly re-worked phenix.refine bug fixes: - Proper handling of chain breaks, to avoid incorrect angle, dihedral, chirality and planarity restraints. This bug was likely to lead to bad restraints for structures with alternative conformations. - Avoid Wilson B crash for no data if low resolution omitted - Proper handling of NCS + remove_h=true - Proper handling of negative residue numbers - Avoid segfault in twin refinement - Cumulative fixes and enhancements in picking and refinement of interatomic scatterers (IAS) phenix.refine vdw_1_4_factor changed from 2/3 to 0.8 (to improve geometry and MolProbity clash scores in particular) phenix.refine obsolete remove_hydrogens option removed New phenix.pdbtools (use --help) Command aliases removed (i.e. mmtbx.xtriage is now only available as phenix.xtriage) Most major commands renamed to phenix.*, e.g. iotbx.emma -> phenix.emma iotbx.pdb.hierarchy -> phenix.pdb.hierarchy Use phenix<TAB> (in most shells) to get a full list of available phenix commands. eLBOW - Perform simple eLBOW jobs in COOT - Automatically perform the appropriate calculations on all the unknown ligands in a PDB file and combine the CIF results into one file - Covalent bonding of ligands to macromolecules (phase I implementation) - Print the sequence of PDB file (elbow.print_sequence) - User control of addition and writing of Hydrogens - Output of TRIPOS mol2 files - User control over naming of output files - elbow.join_cif_files has re-ordered arguments (target as last argument) - elbow.link_edits will generate "edits" from PDB LINK records for input to phenix.refine - elbow.metal_coordination will generate phenix.refine "edits" for metal coordination spheres including angles

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