- phenixbb - phenix-online.org

(no subject)
by Thomas C. Terwilliger 22 Aug '08

22 Aug '08

Dear Colleagues, The ICSG 2008 International Conference On Structural Genomics is coming up Sept 20-24 in Oxford, UK. We have a terrific program lined up and I hope that you'll register now if you haven't already! I've copied the latest announcement of the meeting below. All the best, Tom Terwilliger ISGO International Conference On Structural Genomics, Oxford 2008 Web site: http://www.spine2.eu/ISGO 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. Keynote Speakers: Ian Wilson Dino Moras Chas Bountra Peter Donnelly Session Topics - ( See http://www.spine2.eu/SPINE2/ISGO/ for details) Structural genomics, systems biology and complexes Generating insight into protein function with structural genomics SG technologies: methodologies and dissemination The impact of structural genomics on treating diseases Structural determination, methods and computational tools International funding, co-operation and visions for the future 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 Social program reservations closing date: August 31st (Blenheim Palace Dinner) Registration form: http://www.spine2.eu/SPINE2/ISGO/register 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 is now open

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Re: [phenixbb] cci_apps on irix
by o.h.weiergraeber＠fz-juelich.de 22 Aug '08

22 Aug '08

Hello Nat, thanks for your suggestions. Yes, I have used these tricks before, but sadly, the cci_apps build system ignores them completely. As far as I can see, there is no "central" place to set these variables, and the component packages behave differently. The cleanest way to go would be to just correct the syntax problems. Until recently, cci_apps was available as a precompiled irix package (and I think it was mipspro), so maybe one of the developers could comment on the specifics of this compilation. Thanks Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ----- Original Message ----- From: Nat Echols <NEchols(a)lbl.gov> Date: Friday, August 22, 2008 4:57 pm Subject: Re: [phenixbb] cci_apps on irix ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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phenix.pdbtools
by Jianghai Zhu 20 Aug '08

20 Aug '08

Hi, I am trying to use phenix.pdbtools to calculate the geometry statistics for a model from Rosetta. "phenix.pdbtools --show-geometry- statistics foo.pdb" stopped with a message "Sorry: Number of bonds with excessive lengths: 707". Anybody know what happened there? Thanks. -- Jianghai

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placing ligands in coot with phenix.elbow output
by Feldman III, George Franklin 20 Aug '08

20 Aug '08

Hi all, I am having difficulties with my ligand. My ligand is an FMN (flavin mononucleotide) and its pdb file was originally created using PRODRG. I used the DRGFIN.PDB output file to run elbow (phenix.elbow DRGFIN.PDB --opt). The output contains hydrogens, which as we all know do not work well with coot. So when I try to place my ligand in its correct position and save the coordinates in coot, I get an error of duplicated atom labels when trying to merge the molecule to the ligand using phenix.refine. I tried using the command "phenix.elbow DRGFIN.PDB --opt --write-hydrogens=False" but phenix told me that last command doesnt exist (although its posted on the web page). Manually changing the atom names will affect both the connectivity and the cif file (I think), so it is an option I would rather avoid. Is there a way around all of this? Best Regards, George (Trey) Feldman

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Re: [phenixbb] [phenix] generate r free flags in phenix.refine not obeying high resolution limit?
by Pascal EGEA 20 Aug '08

20 Aug '08

Hi All, Following Pavel's answer to Francis Reyes, I have a very basic question about this too. What is a good distribution of reflections and what are thin bins of resolution to ensure correct ML estimations? Are there any basic statistical rules that should be considered. Thanks Pascal Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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generate r free flags in phenix.refine not obeying high resolution limit?
by Francis E Reyes 20 Aug '08

20 Aug '08

Hi all When generating R-Free flags from phenix refine, flags are generated all the way to the limit of the data. However, shouldn't flags be generated up to the limit of the data if specified via refinement.input.xray_data.high_resolutio n ? If not, are the statistics for R/Rfree matching to high resolution data that may be suspicious ? 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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(no subject)
by Sudharsan Sridharan 20 Aug '08

20 Aug '08

Hi all, A quick question about extracting info/preparing pdb file for deposition.......... I've got a pdb file after refinement using phenix 1.3b. I was wondering if there is a way to prepare this file / format this the same way as in 1.3 final where we get "REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP" and REMARK 3. i'm already running refinement 1.3 final with the same parameters just to quickly compare the resulting refined files/numbers. I guess I could do it manually but curious if there is an easier way using 1.3 final. thanks, Sid.

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Resolution cutoffs. Always debated?
by Francis E Reyes 19 Aug '08

19 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 18 Aug '08

18 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 18 Aug '08

18 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 18 Aug '08

18 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 17 Aug '08

17 Aug '08

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PHENIX 1.3 Available
by Paul Adams 17 Aug '08

17 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 15 Aug '08

15 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 15 Aug '08

15 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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phenix.twin_map_utils AssertionError
by hari jayaram 14 Aug '08

14 Aug '08

Hi I am trying to run the following command phenix.twin_map_utils data.file=cy_p10_2_28.1_unique1.mtz model.file=cy_p10_2_28.1.pdb obs_labels=F_p10-2,SIGF_p10-2 free_flag=FreeR_flag When I run phenix.twin_map_utils from phenix version 1.3 final or from the newest cci_aps. I get the following AssertionError ( see below). I think my mtz file is kosher because phenix.refine with the twin_law option handles it well and I can refine with a twin law. Is there something wrong in the syntax or the file. I am attaching the log file with the Assertion Error to this email. Thanks for your help Hari Overall and bulk solvent scale paranmeters and twin fraction estimation ======================================================================= Traceback (most recent call last): File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/command_line/twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/twinning/twin_map_utils.py", line 306, in run out=log) File "/Users/hari/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 946, in __init__ assert self.f_obs.indices().all_eq( self.free_array.indices() ) AssertionError

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phenix pdp files and coot - FIXED
by nihmmayerm 13 Aug '08

13 Aug '08

Hi, The problem was that coot choked on the TER and BREAK lines in the PDB, once I removed these 0.4.1 reads the phenix PDBs fine. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I've just finished refinements with latest version of phenix (/phenix-1.3-final/build/mac-intel-osx/bin/phenix) in which I used riding hydrogens added with reduc (Molprobity) version and TLS - so I have anisou records - and a bunch of acs. When I open files in coot (coot/0.4.1/bin/coot) I see only 1 chain (I have a dimer chain A and B) and no solvent or other heteroatoms. The file displays fine in pymol - but I want to rebuild with coot. Any ideas ? I'm using the SBGrid install of coot, and a local installation of phenix. Thanks - Mark

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phenix pdp files and coot
by nihmayerm 13 Aug '08

13 Aug '08

Hi, I've just finished refinements with latest version of phenix (/phenix-1.3-final/build/mac-intel-osx/bin/phenix) in which I used riding hydrogens added with refine (Molprobity) version and TLS - so I have anisou records - and a bunch of acs. When I open files in coot (coot/0.4.1/bin/coot) I see only 1 chain (I have a dimer chain A and B) and no solvent or other heteroatoms. The file displays fine in pymol - but I want to rebuild with coot. Any ideas ? I'm using the SBGrid install of coot, and a local installation of phenix. Thanks - Mark

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Segmentation fault with twin-law refinement
by hari jayaram 13 Aug '08

13 Aug '08

Hi I have discovered that my data in the P3 spacegroup is potentially twinned. Truncate and phenix.xtriage indicate that the twin fraction is pretty high ( between 0.35 and 0.42). I am still new to twinned data refinement and still dont know which twin law to pick from the three possibilities for P3 that xtriage lists. I am emailing because , Regardless of the twin law I try , phenix.refine crashes with a Segmentation fault on my Mac Pro leopard 10.5.2 running phenix. 1.3b-rc6 The command that ends with a Python crash and segmentation fault is Command used: phenix.refine cy_p10_2_28.1.pdb cy_p10_2_28.1_unique1.mtz simulated_annealing=true model.ncs refinement.main.ncs=true --overwrite refinement.ncs.excessive_distance_limit=None strategy=group_adp+individual_sites twin_law='-h,-k,l' refinement.input.xray_data.labels=F_p10-2,SIGF_p10-2 > phenix_run2_mhmkl_simulanneal.log phenix.xtriage outputs Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.100 | 0.406 | 0.407 | 0.393 | | h,-h-k,-l | M | 0.071 | 0.426 | 0.439 | 0.458 | | -k,-h,-l | M | 0.090 | 0.411 | 0.417 | 0.415 | ------------------------------------------------------------------ Can you tell me if there is something I am doing wrong . Thanks a tonne for your help Hari Jayaram Postdoc , Brandeis University

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phenix.reduce
by Mayer, Mark (NIH/NICHD) [E] 12 Aug '08

12 Aug '08

Hi, Does phenix.reduce correctly handle pdb files with alt confs? I ran reduce on such a file ang got a warning that only A was used, and when i checked output there were no H on AC B residues. I then sent file to Molprobity server, ran reduce, and now there are H on residues for both ACs. I'm doing this so I can refine with riding hydrogens. Thanks MLM

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secondary structure restraints
by Nikos Pinotsis 11 Aug '08

11 Aug '08

Dear all, I am refinining a 3.5 A structure where several of fragments are already determined in higher resolution (similar to the case I found below). In addition a large part of the structure is quite disordered (two out of four chains). I found a reply about a year ago that secondary structure restraints are not implemented in phenix, is there any new developements that can help the refinement in low resolution? (I have already employed NCS other common posibilities). thank you in advance for any help and best regards Nikos >/ On May 4, 2007, at 5:10 PM, Pavel Afonine wrote: />/ />>/ Hi Jianghai, />>/ />>/ I see several possibilities to think about or/and try out: />>/ />>/ 1) Fix the coordinates of atoms in the domains for which the high />>/ resolution structure is available and refine the rest; />>/ 2) Refine the domains for which the high resolution structure is />>/ available as rigid bodies and for the rest refine individual parameters; />>/ 3) There is no specific option in phenix.refine to restrain the />>/ secondary structure elements, however there is a tedious way of doing />>/ this (according to Ralf) by defining custom bonds and angles between />>/ specific atoms forming the secondary structure motifs. Look />>/ "Definition of custom bonds and angles" in the latest CCI Apps />>/ phenix.refine documentation for technical details. />>/ />>/ You can perform "1)" and "2)" in ONE refinement run by combining />>/ several refinement strategies and using specific selections for />>/ refinable parameters. />>/ />>/ Overall, at 3.8A resolution the refinement of individual atomic />>/ parameters (coordinates, B-factors) is questionable. I would consider />>/ to try to refine group parameters for B-factors (trough TLS or/and />>/ group B (like one B per residue)) and try to switch between rigid />>/ body refinement of smaller fragments of your model and refinement />>/ individual positional parameters or mix of individual and rigid body />>/ refinement. />>/ />>/ Also, I will think about making a specific option for automatic />>/ generation of secondary structure restrains. However, given the />>/ amount of work it may require this option will not appear in near future. />>/ />>/ Pavel. />>/ />>/ />>/ Jianghai Zhu wrote: />>>/ Hi all, />>>/ />>>/ I am refining a low resolution structure (~3.8 A). For some of the />>>/ domains in the structure, we already have high resolution />>>/ structures. Despite of some conformational changes in some loops, />>>/ the core structures should be the same. I am wondering if it is />>>/ possible to restrain the secondary structures in phenix.refine. />>>/ />>>/ Thanks. />>>/ />>>/ Jianghai/ -- --------------------------------- Dr. Nikos Pinotsis Section of Structural Biology Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB, UK Tel: +44 20 7153 5453 / 5447 --------------------------------- The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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dihedral error
by Simon Kolstoe 08 Aug '08

08 Aug '08

phenix.refine keeps on stopping with the error: AssertionError: Conflicting dihedral restraints: tor id: var_002 1. definition from: residue: DRG, conformer A 2. definition from: residue: DRG, conformer A atoms: " CB DRG A 500 " " OG1 DRG A 500 " " PAL DRG A 500 " " OAF DRG A 500 " It is for a phospho-threonine residue whose dictionary I made in PRODRG. I've tried all the different charge states of the phosphate however phenix gives the same error every time. Any ideas? Thanks, Simon

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ncs in phenix.autobuild
by wang kaituo 07 Aug '08

07 Aug '08

Hi all, I failed in running phenix.autobuild. The end of the logfile said : ______________________________________________________ Build cycle 2 of 11 method:rebuild ...Using simple_ncs_from_pdb to find NCS Residues expected: [62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74] Residues found : [] ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Did not find expected residues in get_xyz_list _____________________________________________________________ The two ncs chain sequence is not exactly same , some sidechain missing and some connectivity not well. But the residue 62-74 is there in both chains. Have the ncs group to be exactly same to find NCS? how can i fix this? ps: phenix.simple_ncs_from_map works well with my pdb. using the ncs_spec file also not works many thanks kaituo

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