February 2014 - phenixbb - phenix-online.org

exporting results, reduce
by jp d 10 Feb '14

10 Feb '14

hi, we have a large complex at low resolution (7A) and just want to see general conformational changes. Occasionally phenix gets stuck at 'Exporting Results' and top shows 'reduce' running and using lots of RAM . so much RAM that it starts using swap. is there a way to bypass or limit the reduce step. thanks jpd

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ACA2014 Albuquerque
by Peter Zwart 10 Feb '14

10 Feb '14

Dear All, This May 24 to 28, the ACA meeting in Albuquerque will be host to an exciting scientific program. There will be workshops covering (Grazing Incidence) Small Angle Scattering, Joined X-ray/Neutron Crystallographic Refinement and the visualization of diffraction data. The Transactions sessions will celebrate the impressive legacy of the first 100 years of Crystallography.The scientific sessions will feature the latest developments in crystallography and scattering methods and is host to host an impressive list of speakers, such as John Helliwell (Patterson Award),Wayne Hendrickson, Axel Brunger, Richard Neutze and Borden Lacy (Etter Early Career award). We are still accepting the submission of abstracts and we encourage you to do so as quickly as possible: (most of) the session leaders have not finalized their session program yet, so there still is an opportunity to get selected to give a talk. Regards Christine Beavers & Peter Zwart

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Running Phenix on a small cluster
by Mads Beich-Frandsen 10 Feb '14

10 Feb '14

Dear all, We have a small cluster running Ubuntu, using the Condor distribution package. –Does anyone have experience in setting up Phenix to run in such an environment? Thanks in advance, /Mads ******************************** Mads Beich-Frandsen, PhD Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain Tel: +34-9340-37188 | Fax: +34-9340-39960 E-mail: mads.beichfrandsen(a)irbbarcelona.org

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RNA sugar pucker
by Benoît Masquida 08 Feb '14

08 Feb '14

Hello everyone, Does someone know how to define the sugar pucker in eLBOW? I am trying to force a C3' endo conformation for GDP. Thanks for your help. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

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Meeting Announcement: Northwest Crystallography Workshop
by Dale Tronrud 07 Feb '14

07 Feb '14

(Pacific) Northwest Crystallography Workshop http://oregonstate.edu/conferences/event/nwcw2014/ June 20-22, 2014 Registration is now open for this year's edition of the Northwest Crystallography Workshop. It is being hosted at Oregon State University in Corvallis in the heart of the Willamette Valley surrounded by wine country, wildlife refuges, and with both the Cascade Mountains and the Pacific Ocean within easy driving distance. It can be easily accessed from either the Portland or Eugene airports. This biennial meeting has been held at various locations in the Pacific Northwest since 1981. It has always proven to be a great venue to meet other researchers in the region who are interested both in using macromolecular crystallography to solve structures and in developing and enhancing methods. The "workshop" part of the name will be taken seriously. We will have talks and posters with priority for speaking slots given to students and post-docs who focus on methodologies or interesting structure determination stories, and/or how structural observations provide insight into function and biology. There will be a reception on Friday evening. On Saturday there will be talks during the day and a banquet followed by a keynote address in the evening. Talks will continue on Sunday morning with the workshop wrapping-up at noon. A light lunch will be served on Saturday and a boxed lunch will be available on Sunday. Register today and get your abstracts submitted anytime between now and the April 30 abstract deadline. We've tried to keep registration costs low and early registration (through April 30) is $75 for students and $100 for others. Reasonably priced on-campus dormitory housing is available and must be arranged at the time of registration. Special rates at two local hotels have been arranged for those who want to book their own lodgings. We look forward to a great meeting and celebration of the International Year of Crystallography. Dale and Andy Dale E. Tronrud and P. Andrew Karplus Department of Biochemistry & Biophysics 2011 ALS Bldg Oregon State University Corvallis, OR 97331 USA

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how to remove hydrogen from pdb
by Afshan Begum 07 Feb '14

07 Feb '14

Dear Experts, Could you kindly tell me how can i remove hydrogen from my coordinate. Actually i refine my structure with phenix along all hydrogen now its almost done but before submitting the molecule into PDB data bank i want to remove hydrogen from the coordinate which i do not know how to do, suggestion would be appreciated Best Regards AFSHAN =========================================== Dr. Afshan Begum

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weight_selection_criteria
by Mark A Saper 06 Feb '14

06 Feb '14

Can anyone explain what the weight_selection_criteria parameters (see below)? How do they interact with other weights. Are they still used if I set optimize_xyz_weight=TRUE? I'm using dev-1616. target_weights optimize_xyz_weight= False optimize_adp_weight= False wxc_scale= 0.5 wxu_scale= 1.0 wc= 1.0 wu= 1.0 fix_wxc= None fix_wxu= None shake_sites= True shake_adp= 10.0 regularize_ncycles= 50 verbose= 1 wnc_scale= 0.5 wnu_scale= 1.0 rmsd_cutoff_for_gradient_filtering= 3.0 force_optimize_weights= False weight_selection_criteria bonds_rmsd= None angles_rmsd= None r_free_minus_r_work= None r_free_range_width= None mean_diff_b_iso_bonded_fraction= None min_diff_b_iso_bonded= None Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan c/o Biophysics, Chem 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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phenix version 1.8.4
by Rosario Recacha 06 Feb '14

06 Feb '14

Hello, I installed the last version if phenix in ubuntu and whe I want to run it I receive the next message: ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory I installed older versions in other computers following the same indications, and never I have had problems. Thanks in advance. Kind Regards, Rosario

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phenix.autosol and phenix.hyss now optimized for weak SAD data
by Terwilliger, Thomas C 06 Feb '14

06 Feb '14

Hi Phenix users! You might notice some big differences in HySS and AutoSol in the new 2014 versions of Phenix (starting with current nightly builds and the soon-to-be-released Phenix-1.8.5). The big changes are parallelization, the use of Phaser completion in HySS, iterative Phaser completion using maps and models in AutoSol, and on-the-fly optimization of parameters in AutoSol for cases with weak anomalous signal. Now HySS and AutoSol can solve structures with very weak SAD phase information that previous versions could not solve. More details will be in the Phenix newsletter that will come out shortly! You can see documentation on the new HySS at: http://phenix-online.org/version_docs/dev-1613/hyss.htm#anch8 and on the new AutoSol at: http://phenix-online.org/version_docs/dev-1613/autosol.htm#anch118 --Tom Terwilliger, Randy Read, Gábor Bunkóczi, Nat Echols

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Computational Crystallography Newsletter - Volume 5, Number 1
by Nigel Moriarty 05 Feb '14

05 Feb '14

Dear Colleagues, I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. Articles -------- FEL Detectors and ImageCIF Quantum Mechanics-based Refinement in Phenix/DivCon Short communications -------------------- Short Communications Phenix tools for interpretation of BIOMT and MTRIX records of PDB files Coping with BIG DATA image formats: integration of CBF, NeXus and HDF5 Fitting tips #7 - Getting the Pucker Right in RNA Structures Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, 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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