April 2008 - phenixbb - phenix-online.org

random seed to phenix.reflection_file_converter
by iulek＠interponta.com.br 18 Apr '08

18 Apr '08

Hi, Is there a way to provide a random seed to "phenix.reflection_file_converter" such that two runs will produce the same result (the same reflection set flagged as free)? What would be the syntax? For while I could only find for the context of refinement and simulated annealing ... Thanks, Jorge

5 4

questions about twinned structure and MR
by Christina Bourne 18 Apr '08

18 Apr '08

Hello bb, I am new to Phenix and am facing my first twinned structure. While I wait for my copy of Yeates Methods in Enzymology (albeit from 1997) to be delivered, perhaps this bb could answer a few questions? At what point do I detwin, or do I not do it at all? It seems Phenix does this itself, on the fly? Is it refining the twin fraction too? MR (Phaser) finds solutions with twinned or detwinned data. However, the solutions vary by 180degrees, so I suspect I'm finding solutions for both h,k,l and h,-k,-l. These come from two different runs, but one has refined LLgain of 1010.8 (matches soln found with detwinned data, both run through ccp4), and other has refined LLgain of 1073 (through Phenix; it's rotated 180degrees from the other). When performing AutoBuild after AutoMR, should I worry that I haven't assigned Rfree? Does Phenix account for twinning when it does this automatically, or what keyword(s) do I need to include? I see a section in the documentation about refining twinned structures, and am looking forward to getting to that point! I just want to be sure I'm following a "correct" procedure for the steps leading up to that. From the literature, it seems quite common to not account for twinning until refinement. My concern is the two MR solns...which should I use? If I know it's twinned, shouldn't I account for that from the beginning? More details: P41, data good to 2.2A, 2 molecules in the AU, twinning fraction ~0.4. Rmerge from scaling is reasonable at ~11% overall. MR model is 100% identical to this data, but from a different spacegroup (thus I'm running MR). Thanks for any tips or guidance! Christina Bourne ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

2 1

Phenix on Altix 350 ?
by Sankar Narayanan Manicka 16 Apr '08

16 Apr '08

Sir, I would like to install Phenix on an SGI Altix 350 server with five 64 bit intel itanium processors. How do i proceed ? sincerely sankar -- ****************************************************************** Sankar N. Manicka C/o Prof. S. Krishnaswamy Dept. of Genetic engineering School of Biotechnology Madurai Kamaraj University Madurai 625 021 TN INDIA mailto: sankar(a)mkustrbioinfo.com ******************************************************************

6 8

how to avoid self disulfide bond in phenix refinement?
by Chen Chen 14 Apr '08

14 Apr '08

Hi, I am having a problem in phenix.refine. I ran phenix.refine --dry_run foo.mtz foo.pdb The program generate a parameter file named foo.param. I made some modification of foo.param. Then ran phenix.refine foo.mtz foo.pdb foo.param The program reports a weir error message: ========================== Set up restraints manager ========================== Number of disulfides: simple=3, symmetry=0 Simple disulfide: " SG CYS A 29 " segID="A " - " SG CYS A 29 " segID="A " distance=0.00 Simple disulfide: " SG CYS A 180 " segID="A " - " SG CYS A 180 " segID="A " distance=0.00 Simple disulfide: " SG CYS A 286 " segID="A " - " SG CYS A 286 " segID="A " distance=0.00 ... Sorry: Bond restraint model distance < 0.001: Please inspect the output above and correct the input PDB file. ======================================================================== It seems that the program recognized three "self-disulfide" bonds. This problem happens even I do not make any modification in foo.param. However, if I just ran phenix.refine foo.mtz foo.pdb with every parameter at default, the programs runs OK without the above error. I am wondering if it is a bug or if I made some mistakes. Thanks Chen -- Chen Chen, Ph. D., Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 Office Phone: 240-314-6122

3 2

Searchable phenixbb
by Mark Collins 11 Apr '08

11 Apr '08

Hi phenix community Is there a search function for this bb, as there is for the ccp4bb? I have some questions about twinning, TLS and alternate conformations in phenix.refine. I hate repeating questions that have been answered previously but going thru the Archives month by month is proving to be a little slow. Thanks Mark Collins

4 6

Persistence of CONECT records?
by Warren DeLano 10 Apr '08

10 Apr '08

Though I wouldn't mind PyMOL taking credit for CONECT valence encoding, this was in fact a convention originally employed by MacroModel which I adopted from Schrodinger. According to OpenBabel maintainer Geoff Hutchinson, it is also a convention supported by the OpenBabel chemical interchange software, and it according to OpenEye's docs, OEChem supports it as well (with the OEPDBFlag::ORDERS, BONDS, and BOTH flags to OEWritePDBFile). Given that four popular tools already support this convention, shouldn't PHENIX do so as well? ________________________________ Message: 4 Date: Thu, 10 Apr 2008 12:53:27 -0400 From: "Schubert, Carsten [PRDUS]" <CSCHUBER(a)prdus.jnj.com> Subject: [phenixbb] Persistence of CONNECT records? To: <phenixbb(a)phenix-online.org> Message-ID: <889E20E3723D0C45A493DA5DA87D854E01E876B6(a)JNJUSRAGMS02.na.jnj.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I noticed that the CONNECT records of ligands generated in elbow get deleted in phenix.refine. Even specifing both the protein and ligand file (with CONNECT records) in the .def files, does not retain these records. For us they are coming in handy since they specify the bond order of the ligands. This is important for display in PyMol, which assigns bond orders based on these records. Would it be possible to keep the CONNECT records in the output file of phenix.refine? Obviously the numbering would need to be adjusted and I have not yet checked if some of the model building programs like coot would be able to handle this situation correctly. Cheers, Carsten

2 1

Persistence of CONNECT records?
by Schubert, Carsten [PRDUS] 10 Apr '08

10 Apr '08

Hi, I noticed that the CONNECT records of ligands generated in elbow get deleted in phenix.refine. Even specifing both the protein and ligand file (with CONNECT records) in the .def files, does not retain these records. For us they are coming in handy since they specify the bond order of the ligands. This is important for display in PyMol, which assigns bond orders based on these records. Would it be possible to keep the CONNECT records in the output file of phenix.refine? Obviously the numbering would need to be adjusted and I have not yet checked if some of the model building programs like coot would be able to handle this situation correctly. Cheers, Carsten

2 1

Ignoring SegIDs
by Stephen Graham 10 Apr '08

10 Apr '08

Hi all, Apologies if this is a dumb question, but... Is there a way to get phenix.refine to ignore segids? I ask because COOT seems to be blithely unaware of segids and they have a habit of disappearing when one is rebuilding a model, resulting in very odd geometries when the side chain of a residue is in segment ' ' and the main chain is in segment 'A'. Alternatively, is there a 'convert chain IDs to segids' option like in CNS? Basically, I would like the segids removed/fixed/ignored automagically at the start of refinement (since I never use them for anything useful anyway). Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

3 5

phenix-cns conversion
by Sean Johnson 08 Apr '08

08 Apr '08

What is the best way to convert phases obtained from phenix to a usable cns format? I have 3.6 A maps that were SAD phased and density modified using phenix. I now want to use some of the cns refinement options - like torsion angle refinement. I tried converting structure factors and HL coefficients to cns format using phenix.reflection_file_converter, but when I run cns input files, I start getting errors like the ones shown below (this is from density_modify.inp): _____ Program version= 1.2 File version= 1.2 %XMAPASU-AUTOmem: increasing memory allocation to 2000000 Minimum brick that covers asymmetric unit: A= 0,..., 150 B= 0,..., 150 C= 0,..., 36 Sum of 21042 elements = 21042.0000 SHOW: average of 810150 elements= 0.0000 ANOMalous=FALSe {OFF} XMPST: average = 0.0000 minimum = 0.0000 maximum = 0.0000 XMPST: r.m.s. = 0.0000 norm = 0.0000 XMHISTO: (default from map) RHOMIN and RHOMAX = 0.0000 0.0000 %XMHISTO-ERR: a complete flat map. XMHISTO: (default from map) SLOT width = 0.000000 %XMHISTO-ERR: the SLOT width is too small 0.00000 XMHISTO: the number of slots MBINS=10000 and width SLOT= 0.0000 %XDOTYPE-ERR: Variable/type mismatch: do (masksol=1) (real(automap) <= $cutoff) ^ %DO-ERR: Data type mismatch. Selection must be a logical expression.: do (masksol=1) (real(automap) <= $cutoff) ^ %SHOW error encountered: There were errors in DO expression. (CNS is in mode: SET ABORT=NORMal END) ***************************************************** ABORT mode will terminate program execution. ***************************************************** Program will stop immediately. ______ I'm guessing that the problem has to do with the way I am converting the data to cns (since I have beautiful maps from phenix), but I'm really stuck right now. Any guidance would be appreciated. Thanks, Sean Johnson -- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) sean.johnson(a)usu.edu

2 1

ICSG 2008 Oxford Sept. 20-24, 2008
by Tom Terwilliger 07 Apr '08

07 Apr '08

Dear PHENIX users, I would like to encourage you to attend the 5th International Conference on Structural Genomics Sept 20-24th! This is the principal conference on structural genomics; it occurs every 2 years in a different part of the world. This year's meeting is in Oxford, UK and will have a lot of methods talks in addition to structural biology results. You can register at http://www.spine2.eu/ISGO . I'll look forward to seeing you in Oxford in September! All the best, Tom T The 5th International Conference on Structural Genomics (ICSG 2008) will be held in Oxford, UK on September 20-24th. The biennial Conference is the premier meeting for the Structural Genomics scientific community world-wide and is hosted on behalf of the International Structural Genomics Organization (ISGO) by Professor David Stuart at the University of Oxford, Division of Structural Biology. The Scientific Program will contain main scientific sessions, poster sessions, breakout discussion groups for specific topics and a social program and we expect to attract a worldwide audience of 500 delegates. Provisional Session Topics - Structural genomics, systems biology and complexes - The impact of structural genomics on treating diseases - Maximising impact on and integration with biology - HTP methods for membrane proteins - Hybrid/multidisciplinary approaches - Strategies for intrinsically unfolded proteins - Should we expand the protein universe or concentrate on biology? - New technologies The venue will be in the UK at the University of Oxford Examination Schools, High Street, Oxford. The Schools are in the heart of Oxford, central to all colleges, the main Oxford cultural and shopping areas and close to hotel and college accommodation. Registration and abstract submission is now available. Early registration and abstract submission deadline: 31st July 2008 http://www.spine2.eu/ISGO Social program reservations closing date: August 31st 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

1 0