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wwPDB X-ray validation task force update
by Randy Read 11 Nov '15

11 Nov '15

Dear CCP4 and Phenix BB subscribers, The worldwide PDB X-ray validation task force is being reactivated to consider what updates need to be made to the validation criteria that are reported and the validation reports that are produced when you either deposit a new structure or use the standalone wwPDB validation server. We're already aware of a number of issues. Probably the biggest single issue is improving the validation of ligands, including numerical and visual analysis of fit to density. There's a lot of room for improvement of the validation of carbohydrates. Our agenda also includes discussions on metals, radiation damage and cis-peptides, among other topics. The task force will be meeting this coming Monday and Tuesday, so now would be a good time to provide feedback on the current state of the art and in particular on any aspects that I've left out of that list of the topics we'll be discussing. If you have constructive suggestions on any aspect of X-ray structure validation at the wwPDB, I would be happy to collect any emails I receive and convey them to the rest of the task force. It's also possible to send feedback at any time through the official channel by an email to validation(a)mail.wwpdb.org. * Are there current validation criteria that should be retired in favour of other criteria? * Are there missing criteria that should be added? * Are there ways in which the presentation of the validation results in the report could be clarified? Best wishes, Randy Read ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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mr_rosetta fragment_files by chain
by Perry, Kay H. 10 Nov '15

10 Nov '15

I am trying to run rosetta for a heterodimer with two different chains. I have the following commands, but in some subprocesses, I get the error message: Sorry: Sorry, need 2 fragment files (3 and 9 residues) for rosetta_rebuild I have the following in my script: fragment_files_chain_list=V \ fragment_files_chain_list=A \ fragment_files_3_mer_by_chain="orfx3_03_05.200_v1_3" \ fragment_files_9_mer_by_chain="orfx3_09_05.200_v1_3" \ fragment_files_3_mer_by_chain="orfx1_03_05.200_v1_3" \ fragment_files_9_mer_by_chain="orfx1_09_05.200_v1_3" \ Do I need to have the chain ID in the filename? Kay Kay Perry NE-CAT 9700 S. Cass Ave. Bldg. 436 E007 Argonne, IL 60439 630-252-0692

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error with phenix.refinine
by Maxime Cuypers 08 Nov '15

08 Nov '15

hi, i have the following error refining a neutron structure (no xrays data) with the latest builds (dev and official): it used to work perfectly and now it says: tried many things with my pdb yet to no avail. even archived runs do not work anymore. ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 19.38 23.49 4.11 1.665 13.405 32.138 0.039 Traceback (most recent call last): File "/usr/local/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/command_line.py", line 162, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/driver.py", line 1532, in run call_back_handler = call_back_handler).result File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/strategies.py", line 201, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 117, in __init__ self.call(self.adp, "ADP refinement (reciprocal space)") File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 143, in call func(prefix = prefix) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 396, in adp log = self.log) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/adp.py", line 62, in run h_params = h_params) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 232, in __init__ nproc = nproc) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 337, in __init__ result = self.try_weight(weight, print_stats=True) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 427, in try_weight minimized = self.minimize() File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 496, in minimize self.model.set_refine_individual_adp() File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/model.py", line 1523, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx Internal Error: /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/modules/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. any clue what is happening? thank you for your help, Maxime Cuypers

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Berkeley Server Downtime Cancelled
by Paul Adams 06 Nov '15

06 Nov '15

Dear Colleagues, I’m pleased to report that the scheduled power outage has been cancelled and will be rescheduled for a future weekend. Cheers, Paul -- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Trends In Initial Crystallization Screening
by Mustafa Koksal 06 Nov '15

06 Nov '15

Dear members of the crystallography community, I would like to assess the tendency/trend in our community to outsource initial crystallization screening experiments. Here, outsourcing refers to sending your protein/DNA/RNA sample to a service provider, who will set up crystallization experiments, take images of crystallization drops at various time points, make images available to you, and, if you require, send you the plate to retrieve any crystals. To do assessment, I prepared a short-answer questionnaire, which contains 10 questions and should take less than 5 minutes to complete. I especially encourage the new PIs and young researchers to complete the questionnaire. Could you please fill out the questionnaire at the following link? https://tr.surveymonkey.com/r/BVNCPVV In case you are unwilling to click links in e-mails, I also included the questions here. Please reply with answers in private to: mustafakoksal(a)iyte.edu.tr Thank you very much for your contribution. Mustafa Questionnaire: 1. Have you outsourced initial crystallization screening experiments in any of your projects before? Yes No 2. If you did, what format and type of experiment you used (choose all that apply)? 96 well/plate 384 well/plate 1536 well/plate Sitting Drop Hanging Drop Microbatch Other (please specify) 3. If you did, what price did you pay per 96-conditions? 4. If you did not, what prevented you from outsourcing (choose all that apply)? It is costly Shipping a sample is hard Privacy concerns I prefer to do it in my lab I do not think it is advantageous I do not have enough sample Other (please specify) 5. Would you be interested in outsourcing initial crystallization screening experiments in future? Yes No 6. If you are interested, which method would you prefer (choose all that apply)? Sitting Drop Hanging Drop Microbatch Counter Diffusion Other (please specify) 7. If you are interested, up to what price would you be willing to pay per 96-conditions? $1 $2 $3 $4 $5 $6 $8 $10 $12 $15 $20 $25 $30 $50 8. If you are interested, what would be your minimum-maximum throughput (# of 96-condition experiments per month)? Note: a 1536-condition experiment is 16 x 96-condition experiments? 1 - 2 2 - 4 4 - 8 8 - 12 12 - 16 16 - 32 32 - 64 32 - 128 More than 128 9. How much sample would you be willing to sacrifice per screening 96-conditions (please specify in micrometers)? 10. Would you consider international shipping of your sample for outsourcing? Do you have any other comments? End of Questions -- Mustafa Koksal Postdoctoral Fellow University of Pennsylvania Department of Chemistry Roy and Diana Vagelos Laboratories Office: 2090 IAST Office Phone: (215) 898-2227 Mobile Phone: (267) 319-6443 Mail Address: 231 S. 34th St, Philadelphia 19104, USA --

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(no subject)
by Nigel Moriarty 06 Nov '15

06 Nov '15

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2016 issue is 18 December 2015 (with some leeway if you are still working on the text, especially as it can be polished over the break). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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ERRASER Updates
by Caleb Geniesse 05 Nov '15

05 Nov '15

Hi all, My name is Caleb and I am a research programmer in the Das lab who has taken over the maintenance of ERRASER. ERRASER (Enumerative Real-space Refinment ASsisted by Electron-density under Rosetta) is an application for improving RNA crystal structures based on Rosetta and Phenix. While benchmarking the current state of ERRASER, I uncovered some discrepancies in the clash scores and outliers of the resulting models (compared to the original benchmark in Chou FC et al., 2012). Accordingly, I've made some updates to the ERRASER code within Rosetta addressing these issues. *To avoid possible inaccuracies introduced by these bugs,* *all PHENIX-ERRASER users should download/install a weekly build of Rosetta 2015.35 (released Sept. 24, 2015) or later.* For more extensive PHENIX-ERRASER documentation and installation notes, please see: https://www.phenix-online.org/documentation/reference/erraser.html. Please let me know if you have any questions! All the best, Caleb Geniesse

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Berkeley Server Downtime
by Paul Adams 05 Nov '15

05 Nov '15

Dear Colleagues, as part of routine maintenance at our new building there will be a power outage to the Computational Crystallography Initiative server room. As a result several structural biology web services will be offline for a short while. These include: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) The servers will be shutdown at 5pm Pacific time on Friday November 6th. Services should resume by the evening of Sunday November 8th at the latest. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience. Cheers, Paul -- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Modifying restraints for a single glutamate
by Eric Johnson 05 Nov '15

05 Nov '15

Is it possible to modify the restraints for single glutamic acid residue that forms an ester bond with a heme? Formation of the ester bond should lengthen the C - O bond length. Normal restraints distort the geometry of the covalent adduct. Thanks, Eric Johnson

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Installation problem
by Ricardo Padua 04 Nov '15

04 Nov '15

Hi all, I have the error below when trying to install Phenix in Centos6 running in a virtual machine (VMware workstation 12) in Win7 Enterprise. I've searched for this error in ccp4bb, phenixbb and google but nothing came out. Can anyone enlighten me? Best ========================================================================== Phenix Installation version: 1.10.1-2155 machine type: intel-linux-2.6-x86_64 OS version: 2.6.32-573.el6.x86_64 destination: /usr/local/phenix-1.10.1-2155 # of processors: 8 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-1.10.1-2155/base/bin/python /usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 127 Ricardo

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