- phenixbb - phenix-online.org

mtz test set
by Mark Collins 01 May '08

01 May '08

Hi Everyone, How can I get foo.mtz in which the test set number for R-free is 0 and the working set is say 1. Thanks Mark

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autosol output to electron density figure in pymol
by shivesh kumar 01 May '08

01 May '08

Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh

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Re: [phenixbb] native Patterson peak
by Peter Zwart 01 May '08

01 May '08

31 is not too bad actually. When you have such a PT peak, I would consider only an even number of copies in the ASU. When entering desperate mode, I would try all possible P2x2y2z flavors even though your systematic absences might be clear. Of course, experimental phases could be a good solution. HTH P 2008/5/1 David Garboczi <dgarboczi(a)niaid.nih.gov>: > We have datasets measured on crystals of a 19 kD protein that are > P212121, with cell constants of 66, 75, 136. > > Matthew's considerations say 3, 4, or 5 copies per au are probable. > > xtriage finds a native peak at (0.0, -0.5, 0.036) that is 31 in > height (origin=100) > > No self-rotation function peaks in xprep, that I can understand. > > Is this clearly translational symmetry that is making MR difficult? > > Hints as to how to go forward are welcome. > > thanks, > > Dave > > > -- > David N. Garboczi, PhD > Phone: 301-496-4773 > Investigator, Structural Biology Section (SBS) > Laboratory of Immunogenetics (LIG) > National Institute of Allergy and Infectious Diseases (NIAID) > National Institutes of Health (NIH) > Twinbrook 2/Room 110 > 12441 Parklawn Drive > Rockville, Maryland 20852-1742 > Fax: 301-402-0284 > Email: dgarboczi(a)niaid.nih.gov > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [phenixbb] [ccp4bb] Need Solve/Resolve advice [shameless crosspost to phenixbb]
by Peter Zwart 30 Apr '08

30 Apr '08

Hi, (sorry for the crosspost / jumping between bb's), but I don't like advertising phenix on the ccp4bb. If new to Solve (or old as well), try using phenix.autosol. The gui is relatively intuitive, the command line (at least for SAD) as simple as possible and the documentation is very thorough. Before running autosol, try running xtriage and find out if you have translational pseudo symmetry. If you have more then a single molecule in the ASU, there will be NCS, unless all molecules have *extremely* different conformations. The NCS might not be proper/closed though. HTH Peter 2008/4/30 Megan Guelker <megdg(a)rice.edu>: > CCP4bb subcribers, > > I am a new user to Solve/Resolve and am using it on a Mad dataset. Solve > outputs three sites: > > pdb coordinates fractional coordinates > -15.833 35.392 38.440 0.0486 0.4315 0.1615 > 7.834 76.449 38.475 0.5487 0.9320 0.1617 > 16.310 60.866 37.449 0.5432 0.7420 0.1574 > > I noticed that the fractional coordinates for the first two sites are > separated by 0.5 units in x and y, and they appear to be the same site from > looking at the density surrounding them. I know that Solve can output some > sites with repetition if they are results from different seeds. > > I have tried running Solve again with ADDSOLVE and these sites as input (all > three and combinations of the three) and have not been able to pull out any > additional sites. I have also tried using various resolution ranges for > Solve. The same three sites are always output. > > The FOM for the map produced by Solve is 0.45. Resolve improves the FOM to > 0.66. > > The protein has 148 aa with 4 Se sites per protein. The crystals are in > space group P3221, and there are six copies per asymetric unit. There is no > non-crystallographic symmetry. > > I am a new user to Solve, and haven't been able to find an explanation for > why the output sites are so similar and separated by 0.5 units. Does anyone > have any experience with this type of result? I would appreciate any input > and suggestions on how to locate additional sites. > > Thank you for your consideration, > Megan Guelker > > -- > Megan Guelker > Graduate Student > Rice University > Department of Biochemistry & Cell Biology > 6100 Main St. - MS 140 > Houston, TX 77005 > 713-348-2492 (lab) > megdg(a)rice.edu > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Refining low resolution structure
by Humberto Pereira 29 Apr '08

29 Apr '08

Dear all I was trying to refining a low resolution structure with Phenix. The crystal belongs to the SG P6122 with one monomer per ASU. The monomer contains approximately 270 residues. There isn't any NCS operators. The crystal diffracts up to 4.0 Angstrons, with good statistics, however I have only 4204 unique reflections. I solved the structure by MR by Phaser and the solution was quite reasonably. Initially I performed a phenix refining cicle with SA + rigid body, however the Rs values is very divergent (43 and 59%), so I decided to use the key xray_data.r_free_flags.ignore_r_free_flags=true in order to save my precious reflections with and without SA, and I also use the group_adp., in those cases the R is about 39-40%. I want a help to decide the best refinement strategies for low resolution refinement with phenix. BTW I'm trying to produce some different constructions of the gene, expecting improve the resolution. Thanks Humberto

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optimize_wxc won't run
by Nian Huang 29 Apr '08

29 Apr '08

Dear All, I am a novel phenix user. There is a problem whenever I use option optimize_wxc in phenix. The error message looks like following, ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' I don't know what's the problem. Could it be my installation? Nian Huang, Ph.D. Dept. of Biochemsitry UT Southwestern Medical Center

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"gnomebreakpad": libgnomebreakpad.so: error
by shivesh kumar 23 Apr '08

23 Apr '08

Dear all, We are using Fefora core 8. To start phenix, we give the command phenix in the terminal, after 30-40 minutes it shows the following error message *Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory and after 1hr of this message the GUI comes.There is no problem in running phenix afterwards and also with any other programs like CCP4, CNS etc... I have put this query earlier also and I got reply as follows yum install bug-buddy It didn't work for us.If anyone can suggest the solution, it would be very helpful for us.Thanx in advance. shivesh *

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twinning analysis
by Andreas Förster 23 Apr '08

23 Apr '08

Hey all, I've been digging around with a nasty dataset for a while, twinning, pseudosymmetry, etc. Phenix.xtriage has helped me make some guesses as to what's going on, but phenix.twin_map_utils fails. I used an mtz file obtained from XDS via f2mtz and cad as xray data, like so: phenix.twin_map_utils xray_data.file=blah.mtz model=blah.pdb unit_cell=86.623,86.623,121.357,90,90,120 space_group=P65 Here's the error: Traceback (most recent call last): File "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/command_line/twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/twinning/twin_map_utils.py", line 256, in run tmp_params = utils.r_free_flags_params.extract() AttributeError: 'module' object has no attribute 'r_free_flags_params' I see the error on a recent macbook pro with current cci_apps. How can I get around it? Thanks Andreas ps. I apologize if that question posted to the board earlier. I wrote from a wrong account.

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NCS problem
by Bobby Huether 22 Apr '08

22 Apr '08

Hello, My structure contains 2 protein molecules in the asymmetric unit, and they are related by 2-fold rotational NCS to form a dimer. The refinement is nearing completion (1.7 A) and the solvent molecules are now being included. A blob of density has been tentatively identified as being occupied by glycerol, which was present as the cryo-protectant. The issue is that this blob of density lies on the 2-fold NCS rotation axis, and so we need to use 2 glycerol molecules within this density, each at 0.5 occupancy, to conform to the NCS symmetry. This blob of density lies in a surface pocket formed by residues from both NCS-related proteins. When we build in the 2 glycerol molecules and then use phenix.refine, the two glycerols are pushed out of density. Presumably this is because phenix.refine is interpreting this situation as two glycerol molecules sitting on top of on another rather than interpreting it as being a model for a disordered ligand. Can phenix.refine handle this situation? Thanks, Robert

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Omit map around a ligand
by mathieu Coincon 22 Apr '08

22 Apr '08

Hi, I tried to use phenix.autobuild to generate a SA-omit map around a non-protein residue but I didn't succeed. Can someone give me a recipe? (perhaps with file from the ligand fit examples.... ;-) ) Thanks. Have a nice day. Mathieu. ____________ Mathieu Coinçon Biochemistry PhD Student Université de Montréal (+1)514-343-6111 #5352

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Re: [phenixbb] Phenix on Altix 350 ?
by Sankar Narayanan Manicka 21 Apr '08

21 Apr '08

Dear Sir, Sorry for the delay. It was a long weekend here. the output of /etc/*release SUSE LINUX Enterprise Server 9 (ia64) VERSION = 9 PATCHLEVEL = 3 SGI ProPack 4SP3 for Linux, Build 403r1-0512182217 sincerely sankar Ralf W. Grosse-Kunstleve wrote: >> Yes, I could install the CCI_apps Source without any problem. And i ran >> the file "test_apps" without any problem. >> > > Great! > Chances are the next full Phenix source installer will also work. > > If you get a chance, could you send the output of > > cat /etc/*release > > uname -a > > boost_adaptbx.show_platform_info > > Thanks! > Ralf > > > -- ****************************************************************** 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 ******************************************************************

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random seed to phenix.reflection_file_converter
by iulek＠interponta.com.br 19 Apr '08

19 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

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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

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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 ******************************************************************

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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

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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

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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

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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

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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

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phenix-cns conversion
by Sean Johnson 09 Apr '08

09 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

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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

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"unlimit" command with Phenix GUI -unlimit: descriptors: Can't remove limit (Invalid argument)
by hari jayaram 04 Apr '08

04 Apr '08

Hi I am giving new to Phenix and the Phenix GUI. For starters I am trying to run the prime and switch strategy in Phenix. I know all my inputs are fine (see below) but the program aborts ( GUI turns red ) after a few seconds. I checked the resolve.com file in the directory and it has a command "unlimit" which in Leopard causes the following output to be echoed to the stdout "unlimit: descriptors: Can't remove limit (Invalid argument)" Once I deleted the unlimit command I can run the script just fine from a shell. My question is how can I tweak the Phenix GUI so that I dont have to run everything from the shell by manually editing the resolve.com file. The script that stops the GUI is reproduced here. Thanks for your help Hari Jayaram Postdoc , Brandeis University script: #!/bin/csh setenv SOLVEDIR /usr/local/phenix-1.3b-rc6/solve_resolve/ext_ref_files setenv SOLVEBIN /usr/local/phenix-1.3b-rc6/build/mac-intel-osx/solve_resolve/exe # setenv CCP4_OPEN UNKNOWN setenv SYMOP $SOLVEDIR/symop.lib unlimit # $SOLVEBIN/resolve<<EOF access_file mirima.dat labin FP=F_s3-3 FC=FC PHIC=PHIC FOM=FOM FWT=FWT hklin resolve_input.mtz mask_cycles 5 minor_cycles 10 hklout testpms-resolve.mtz no_build prime_and_switch EOF unlimit returns------------> [mango:hj/s3-3/prime_switch] hari% unlimit unlimit: descriptors: Can't remove limit (Invalid argument)

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Crystallographic Postdoctoral Research Position - Berkeley, USA
by Paul Adams 02 Apr '08

02 Apr '08

A postdoctoral research position is available immediately to work on challenging problems in structural biology: Postdoctoral Researcher Job ID: 21615 Division: Physical Biosciences Date Opened: 3/28/2008 This postdoctoral position will study the structure and function of macromolecular complexes and enzymes using X-ray crystallographic methods. This position will be joint between the Center for Protein Folding Machinery (proteinfoldingcenter.org) and the Joint BioEnergy Institute (www.jbei.org). The biological systems to be studied will include: Type-II chaperonins responsible for the refolding of unfolded proteins in archeal and mammalian cells, Glycosyl transferases responsible for the synthesis of hemicellulose in plants, and Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production. The candidate will have experience with using crystallographic methods to study macromolecules; robotic hardware for performing crystallization trials and imaging trays are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. Essential: Primary duties and responsibilities will include using robotic hardware to perform screens for crystallization conditions. Optimization of crystallization conditions. Biophysical characterization of protein samples using standard techniques, such as dynamic light scattering. Characterization of crystals using the Berkeley Center for Structural Biology beamlines at the Advanced Light Source. Collection and analysis of diffraction data, model building and structure refinement. Extensive email and verbal interaction with other researchers. Marginal: Use of small angle X-ray scattering methods to analyze macromolecular complexes in solution. Essential: Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using crystallographic methods. Experience with crystallization methods. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Marginal: Experience with the use of small angle scattering methods. Familiarity with robotic hardware for crystal growth. 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 Center for Protein Folding Machinery visit: http://proteinfoldingcenter.org/ and the Joint BioEnergy Institute visit: http://www.jbei.org/. For more information about the Berkeley Center for Structural Biology visit: http://bcsb.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 21615. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology 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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TLS, B factors, phenix and refmac
by Mischa Machius 01 Apr '08

01 Apr '08

Hi - Prompted by the recent discussions on B values, TLS refinement and differences between Phenix and refmac, we looked into these matters in more detail. We found that the crux of the problem lies in the fact that TLS and B value refinements are usually decoupled. We have developed a formalism that rolls both TLS and B value refinement into one. Phenix and refmac were modified to carry out the calculations, and the outputs from both programs were made compatible to allow proper comparison of the results. We found that the stability of the refinements is now vastly improved. More importantly, however, due to the reduced number of parameters, these calculations can be carried out to resolutions of 7 Å with meaningful representations of indiviual, anisotropic atomic displacement parameters. This low-resolution limit required reformulating the calculation of Wilson B values, but that is only a minor aspect of our treatment that can be neglected. The new, combined procedure for the simultaneous refinement of TLS/B is called 'TBS' refinement, reflecting all required components: Translation, Bibation, Screw. Interestingly, the ‘T’ component is fairly insensitive to input parameters, whereas the overall quality of the refinement is greatly dependent on the ‘B’ component. The more emphasis is put on ‘B’, the more convincing the results. There is a limit, though. At very high levels of ‘B’, the so-called ‘bibacity limit’, the refinement becomes very unstable, leading to inversion in severe cases. Seasoned crystallographers familiar with the concepts can successfully push the procedure to quite high 'B limits', whereas less experienced practitioners should follow the protocols very carefully. Please contact us for any details. Best - MM -------------------------------------------------------------------------------- Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

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Question about anisotropic refinement of selected waters during automatic solvent update
by Schubert, Carsten [PRDUS] 01 Apr '08

01 Apr '08

Hi, I am trying to refine a couple of waters in a structure anisotropically in the latest version of CCI-Apps (Feb-08) . The selection is: refine.adp.anisotropic = "chain W and (resid 25 or resid 54)" The refinement works fine if "main.ordered_solvent = False". When I enable "main.ordered_solvent" the refinement fails with: "Sorry: Bad (empty or mixed) selection in adp_individual.aniso" during the first update of the solvent in macrocycle 1. A workaround is easy to implement, but I think this kind of scheme should work. Although it has all kinds of tricky implication for the downstream handling of the selection if the residues/waters in questions are deleted.... Cheers, Carsten

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