August 2008 - phenixbb - phenix-online.org

Resolution cutoffs. Always debated?
by Francis E Reyes 20 Aug '08

20 Aug '08

I need to put this in front of (this) crystallographic community. What are the criteria for cutting a resolution for data reduction ? Rmerge, I/sig, mean I/sig, completeness... more? I once believed that I/Sig (not averaged) greater than 2 was the cutoff, but I've read online (particularly http://www.mail-archive.com/[email protected]/msg02576.html) that this is no longer the case because of maximum likelihood. I would love to know why this is the case as well as poll the community on how they cut off their data. Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Autobuild builds more residues after MR?
by Francis E Reyes 19 Aug '08

19 Aug '08

Perhaps a silly question, but suppose after MR, there is additional density to be built (say, another molecule). Will the autobuild after mr build into this new density? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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ALS user meeting
by Peter Zwart 19 Aug '08

19 Aug '08

Dear All, I would like to draw your attention to this years ALS user meeting, held from October 13-15. In particular, the workshop titled "Recent advances in the automation of protein crystallography" might be of interest to the protein crystallographic community. The workshop consists of a series of short talks and a hands-on session in which various developers and beamline staff will demo latest developments on their beamlines. Scheduled speakers include: Gyorgy Snell (Takeda SD) Aina Cohen (SSRL) Jay Nix (ALS beamline 4.2.2) Babu Pothineni ( GMCA cat, APS) Scheduled Demonstrations are (tentative titles only) : * Efficient screening and data collection using Mini & WebIce (Bl. 5.0.n) Peter Zwart, John Taylor & Nick Sauter * Data collection @ 4.2.2 Jay Nix * SSRL & Webice Aina Cohen * Automated structure solution with PHENIX P. Afonine * Elves & 8.3.1 J. Holton Detailed workshop information can be found at http://bcsb.als.lbl.gov/wiki/index.php/ALS2008_Workshop Other workshops of interest held during the ALS user meeting can be found here: http://www-als.lbl.gov/als/usermtg/workshops.html Registration is now open for all participants: http://www-als.lbl.gov/als/usermtg/index.html Greetings Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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sharing the ext_ref_files between multiple installations
by Ben Eisenbraun 19 Aug '08

19 Aug '08

Howdy, I'm wondering if it's possible for me to put the ext_ref_files directory into a shared location and then symlink that directory into multiple PHENIX installations to save some disk space. Are the files specific to a particular PHENIX version? Or to a specific CPU architecture? Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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anomalous difference map calculation option in phenix.refine
by Pavel Afonine 18 Aug '08

18 Aug '08

For many of you who asked for anomalous difference map calculation option in phenix.refine: this is fixed and available in just announced PHENIX release. Pavel.

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MemoryError
by Yingjie Zhou 18 Aug '08

18 Aug '08

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PHENIX 1.3 Available
by Paul Adams 18 Aug '08

18 Aug '08

======================================================================== ===== PHENIX 1.3 Release ======================================================================== ===== The PHENIX developers are pleased to announce that the 1.3 general release version of PHENIX is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ This version of PHENIX includes tools for: - Assessing data quality (phenix.xtriage) - Includes the detection of twinning, tNCS, and missed symmetries - Automated structure solution (phenix.autosol) - Combines automated substructure solution (phenix.hyss) with phasing (Phaser/SOLVE), substructure completion, phase improvement (RESOLVE) and fast initial model building (RESOLVE) - Automated molecular replacement (phenix.automr) - Maximum likelihood molecular replacement with Phaser - Automated protein and DNA/RNA model building/rebuilding (phenix.autobuild) - Combines automated model building (RESOLVE), phase improvement (RESOLVE) and structure refinement (phenix.refine) - Automated ligand fitting (phenix.ligandfit) - Fitting a known ligand or screening against a library of the 200 most common ligands - Structure refinement (phenix.refine) - Maximum likelihood targets, simulated annealing, TLS, constrained occupancy refinement, f'/f'' refinement, water picking, anisotropic B-factor refinement, twinned refinement, automatic treatment of alternate conformations, and joint refinement against X-ray and neutron data - Generation of ligand coordinates and restraints (phenix.elbow/ phenix.reel) - Input formats include SMILES and PDB - Restraints can be manipulated with the phenix.reel GUI Full documentation is available here: http://www.phenix-online.org/documentation/ There is a PHENIX bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium. The development of PHENIX is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. ======================================================================== ===== PHENIX 1.3 Release ======================================================================== ===== -- 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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HL coefficients from phenix.refine?
by William Scott 16 Aug '08

16 Aug '08

Is there a simple way to output HL coefficients in refinement, rather than just map coefficients? William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/

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Re: [phenixbb] Neutron exchangeable hydrogen/deuterium positions diverge
by Anna S Gardberg 16 Aug '08

16 Aug '08

Hi, Pavel. That's good to know. (Not pressure you, but) any idea roughly when that will be? -Anna On Thu, Aug 14, 2008 at 5:32 PM, Pavel Afonine <PAfonine(a)lbl.gov> wrote: > Hi Anna, > > Are they very different? I can easily change the code so phenix.refine makes > them identical. The question is do we really need it? I'm not arguing but > just asking. > > > A quick sampling of a handful of residues showed that the separation > at SER and THR HG/DG positions ranged from 0.37 to 1.2 Angstroem. It > seems to me that those values are too high and that there does need to > be a way to constrain them to (or at least restrain them toward) zero. > The separation at the amide positions was much less - 0.04-0.06 > Angstroem. > > > OK, I will add an option to do this. It will appear in one of the next > PHENIX releases. > > Please let me know if you have any other questions or problems! > > All the best, > Pavel. > >

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Neutron exchangeable hydrogen/deuterium positions diverge
by Anna S Gardberg 14 Aug '08

14 Aug '08

Hello, PhenixBB. I am doing joint x-ray/neutron refinement of a hydrogenated protein crystal soaked in D2O buffers, and I've run into a problem with refinement. I hope you can help. I used phenix.ready_set to add deuterium atoms to the exchangeable hydrogen positions. I ran a perl script to set the initial occupancies of those to 0.5 H and 0.5 D (they had been output as 1.0). When I ran phenix.refine with riding hydrogen positions or with individual hydrogen positions, the H and D atoms refined to different positions. How can I constrain the H and D positions to be identical? Regards, Anna Gardberg -- Anna Gardberg Research Associate, Postdoctoral Center for Structural Molecular Biology Oak Ridge National Laboratory Bldg. 4500S, M/S 6142 Oak Ridge TN 37831-6142 phone: 865-576-2173

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