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large ASU: problem with upper/lower case chain IDs
by Cherepanov, Peter P 26 Mar '08

26 Mar '08

Dear phenix developers, I am new to this list and apologize in advance if the following has been discussed before. Although, I must say, the problem is rather unusual... well, we are trying to refine a structure with 36 protein chains per asu (not much fun, but it is our best crystal form for this protein). The chains are labeled (by phaser) with UPPER and lower case characters. THE TROUBLE IS, phenix.refine confuses upper and lower case chain IDs. Now, although default refinement (no restraint_group definitions) works, it is very important for us to define groups of residues, in particular, for NCS. I tried defining chains using quotes (e.g chain "i"; or chain 'i', or "chain i", etc,etc), which did not help. Phenix chokes on our pdb file also after automatic NCS search (although it finds and defines ncs groups correctly). It is funny, because, the program does discriminate between upper and lower case characters when referring to an element (e.g. it does not accept "element Se" when coordinate file has got "SE" and vice versa). Analogous refinement (and NCS definitions) works great in Refmac; but would like to compare results and also take advantage of simulated annealing in phenix.refine. Is there a quick fix, without tedious relabeling the chains? In principle, we could use upper case characters, followed by digits 0-9 [that works], but this would make the whole process very difficult for a number of reasons; I hope there is way around it, thank you, Peter PS: we are using v1.3b

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ADP high variance
by Daniel Frey 25 Mar '08

25 Mar '08

Hello, I have a good data set to 1.8 A and refined it with the actual version of phenix, including annealing and isotropic bfactors. Checking the B factor variance in coot revealed high differences in about 50% of the residues. Most of them are at the surface, but still there are residues like phenylalanines and valines within the core where the bfactors jump from 25 to 50 from one carbon atom to the other. Changing wu and wxu_scale did not improve the results. A quick check with refmac improved the results, so i guess I am missing the right restraints for phenix. Which parameters should be changed to improve the bfactor variance in phenix? Thanks for your help Daniel Daniel Frey Department of Biochmistry University of Zurich Winterthurerstrass 190 8057 Zurich Switzerland freyd(a)bioc.unizh.ch Tel: +41446355558 www.biochem.uzh.ch/gruetter www.structuralbiology.uzh.ch

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Scientific Writer Position, Berkeley California
by Paul Adams 24 Mar '08

24 Mar '08

= = ======================================================================== PSI Knowledgebase Scientific Writer, Lawrence Berkeley National Laboratory = = ======================================================================== Scientific Writer/Editor Division: Physical Biosciences SUMMARY: We are seeking an intelligent and motivated structural biologist technology specialist to research, document, and communicate new technologies to the scientific community. This project is part of the NIH-funded Protein Structure Initiative (PSI) Knowledgebase. The position will require interactions with other groups in the Knowledgebase, members of the Protein Data Bank, researchers at NIH- funded PSI centers, scientific journals, and the broader biological research community. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities are promoting new PSI-developed technologies to the broader scientific community, and editing a web portal describing these technologies. 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. DUTIES: Essential - Primary duties and responsibilities will include regular communication with researchers at the PSI-funded structural genomics centers and other programs. Interaction with other groups in the PSI Knowledgebase, members of the Protein Data Bank, researchers at NIH-funded PSI centers, scientific journals, and the broader biological research community. Collecting information describing technologies from other PSI-funded researchers and by the use of web and bibliographic search tools. Writing text that describes new technologies to the broad scientific community. Maintaining and editing written and graphical material on a web site devoted to technology dissemination. Extensive email and verbal interaction with other researchers. Marginal - Analysis of crystallographic data. QUALIFICATIONS: Essential - BS, MS or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using either computation or instrumentation. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Excellent spoken and written English skills are essential. Marginal - Experience with the solution of macromolecular structures using crystallographic or NMR methods. Practical computational analysis of crystallographic data. Familiarity with scripting languages such as Python. To apply: visit http://cjo.lbl.gov/ and search for the keyword PSI or the job number 21575. 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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Beamline Scientist Position, Berkeley California
by Paul Adams 24 Mar '08

24 Mar '08

= = = = = = = ======================================================================== Beamline Biophysicist Scientist/Engineer, Lawrence Berkeley National Laboratory = = = = = = = ======================================================================== Biophysicist Scientist/Engineer Division: Physical Biosciences SUMMARY: As a member of the Berkeley Center for Structural Biology (BCSB), provide technical and scientific support for users at the BCSB beamlines (http://bcsb.lbl.gov) at the Advanced Light Source in Berkeley California. Work with the BCSB group leader and other BCSB scientists and engineers to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation. Participate on projects involving the structure determination of biological molecules and biomolecular complexes. 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. DUTIES: Essential - Provide support for users regarding data collection, processing, archiving, and analysis. Play a role in coordinating and participating in engineering projects to advance the capabilities of the beamlines, with a focus on robotics systems for sample handling. Participate in the development of instrumentation and methodology for biological crystallography. Participate in the design, implementation, and evaluation of collaborative experiments involving biological crystallography. Collaborate with colleagues both internal and external to the Berkeley Lab. Prepare documentation for beamline staff and users. Prepare scientific data for publication in refereed journals and present findings at seminars and conferences. Required to occasionally work off-hours and weekends to support users. Marginal - Assist with developing research proposals that lead to continued funding in the area of biological crystallography for the BCSB/ALS. QUALIFICATIONS: Essential - Substantial experience working in the area of synchrotron science using complex instrumentation and computer controls. Experience with robotics hardware and control systems. Experience with the collection of experimental data for biological crystallography. Demonstrated ability to conduct independent research and organize results for publication and presentation documented by publication record in either: physics, biology, bioengineering, biophysics, biochemistry or instrumentation fields. Excellent written communication skills along with strong organizational, analytical, and interpersonal skills. Experience in the use of computer programs required for biological crystallography. Ability to work in a team environment and effectively interact with a broad range of colleagues. Marginal – M.S. or Ph.D. in physics, biology, bioengineering, biophysics, or related field. Experience in UNIX computing. To apply: visit http://cjo.lbl.gov/ and search for the keyword BCSB or the job number 21576. 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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Perfect Twins and Ligand Fit or AutoBuild
by Mary Fitzgerald 20 Mar '08

20 Mar '08

I've got a perfect merohedral twin that is refining quite nicely using phenix.refine. In my detwinned FoFc maps, I see density for for a previously diordered region of protein and at least one ligand I soaked in, possibly more. If possible, I'd like to automate the placement of the ligand and build of the diordered region. The data is 3A so it might not work all that well. From looking at LigandFit( I haven't taken a close look at Autobuild yet), I don't see a way to tell the wizard I have twinning. So, can I use Ligand Fit or Autobuild with twinned data? Will the wizards work if I feed it detwinned data and is there a way to get phenix.refine to output the detwinned data other then as map coefficients? Another question/comment. Can I make detwinned 3Fo-2Fc maps? When I tried using the February version of cci_apps, I got an error when I changed the coefficients on my maps in my phenix.def file. Thanks, Mary

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How to use the STIR command in phenix.refine?
by nick＠silvaggi.com 13 Mar '08

13 Mar '08

Hello, I am refining a high-resolution X-ray structure and I would like to gradually increase the resolution from 1.5 to 1.0A, as I used to do in shelxl. I know the STIR command is the way to do this, but I cannot figure out the syntax to use. Currently I am using the following commands: high_resolution = 1.0 low_resolution = None stir = 1.5 When I run phenix.refine (2008_02_08_1610) it echos a line that says "STIR 1.5" before the first macrocycle, but at each stage I see "(resolution: 1.00 - 21.77)." Obviously I am not using the STIR command correctly. Any advice would be greatly appreciated. Thanks in advance. Nick Silvaggi Department of Physiology and Biophysics Boston University School of Medicine 715 Albany St. R-702 Boston, MA 02118

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Beam Time at BCSB beamlines in Berkeley
by Peter Zwart 13 Mar '08

13 Mar '08

============================================================= Synchrotron Beam Time available for Macromolecular Crystallography at Berkeley Center for Structural Biology Beamlines (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2). The ALS is now accepting General User applications for May/June ============================================================= The Berkeley Center for Structural Biology (BCSB) operates five beamlines at the Advanced Light Source in Berkeley. Beamlines 5.0.1, 5.0.2 and 5.0.3 are equipped with the Berkeley Automounter system. Beamline 8.2.2. has a Rigaku Actor sample mounter capable of handling Rigaku, unipucks and ALS style pucks. Beamlines 5.0.2, 5.0.3, 8.2.1 and 8.2.2 have large 3x3 Q315 or Q315r CCD detectors. Beamlines 5.0.2, 8.2.1 and 8.2.2. are MAD stations, whereas 5.0.3 and 5.0.1 are fixed energy beamlines at the Se high energy remote, suitable for Se-SAD experiments. The beamlines generate between 1.5x10^11 and 8x10^11 photons per second of flux into a 100 micron collimator at 1.5 mrad divergence. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for beamtime at these, or any other ALS macromolecular crystallography beamlines, please submit a General User proposal by March 15, 2008 in order to be considered for the May-June schedules. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize You can also request access to any open beam time on the five BCSB beamlines by e-mailing our scheduler at SLOrtega(a)lbl.gov. Any industrial or academic group interested in becoming part of the Participating Research Team for beamlines 5.0.1 and 5.0.2 should contact the Head of the BCSB (Paul Adams: PDAdams(a)lbl.gov, 510-486-4225). (Please note that executed user agreements and proprietary fees, if applicable, must be received at least five working days prior to scheduled beam time.) -- Peter Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron road, Berkeley, CA-94720 Cell: +1 510 289 9246 Fax: +1 510 486 5664

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Collaborative Crystallography
by Banumathi Sankaran 12 Mar '08

12 Mar '08

The Berkeley Center for Structural Biology (BCSB) is pleased to announce a new Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists are able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program provides a number of benefits to researchers: * Obtain high quality data and analysis through collaboration with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. CC proposals go through the regular ALS General User proposal review process. They are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the projects to fit into the available resources. Please note that only non-proprietary projects are currently being accepted. In keeping with similar programs the BCSB staff researchers who participate in data collection and/or analysis should be appropriately acknowledged as authors on publications and/or PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography How To Apply: To submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for Mai/June, 2008, proposals must be submitted by March 15, 2007. Questions: For comments or questions, feel free to contact Banumathi Sankaran (BSankaran(a)lbl.gov) or Gari Kloss (MKloss(a)lbl.gov)

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refine error when optimize_wxc w/o optimize_wxu turned on
by shi jiahai 11 Mar '08

11 Mar '08

Hi, Dear all, I was using phenix.refine to refine the structure. Once I turned on optimize_wxc w/o optimize_wxu, the job failed with the following message. ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/Application/phenix/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 "/Application/phenix/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 "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc The phenix I used is the latest version, 1.3b rc6. The platform is intel-linux-2.6 redhat-e4. Python is 2.4.2 Could anyone please tell me what the problem is? Thank you very much! -- Best Regards, Shi Jiahai

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autobuild errro message
by Christine Gee 05 Mar '08

05 Mar '08

Hi I was using phenix.autoMR and when it tried to go on to autobuild the job ended with the following error message AutoBuild Input failed can only concatenate list (not "str") to list There are two molecules in the asymmetric unit. I tried running phenix.autobuild with the output pdb from molecular replacement and got the same message. The file looks OK to me though. Can you tell me what the problem is? Regards Christine

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