- phenixbb - phenix-online.org

Re: [phenixbb] PHENIX atom selection language
by Kay Diederichs 09 Oct '11

09 Oct '11

Am 09.10.2011 04:20, schrieb phenixbb-request(a)phenix-online.org: > Date: Thu, 6 Oct 2011 18:19:34 -0400 > From: Jianghai Zhu<jzhu(a)idi.harvard.edu> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] PHENIX atom selection language > Message-ID:<E21B0319-CC1D-47A6-9F23-4493700B319C(a)idi.harvard.edu> > Content-Type: text/plain; charset=us-ascii > > Cool. Thanks, Pavel. It would be nice to have a list of all selection keywords and corresponding definitions somewhere. > > -- Jianghai Hi Jianghai, anybody can contribute to the CCP4 wiki, where a Phenix article already exists - check out <http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#Atom_sel…> Unfortunately the wiki is hit by spammers, and we regularly delete whole batches of these pseudo-"users" to keep the userlist clean. The spammers use @gmail.com and @hotmail.com email addresses which we now do not accept any more as new users' email - such addresses are just too easy to obtain. So if you would like to contribute make sure a) to use a email adress of your institution (e.g. university) b) and to contribute to an existing article or start a new one since we won't delete "real" users HTH, Kay

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Re: [phenixbb] Simulated annealing composite omit map conversion
by Yuri 09 Oct '11

09 Oct '11

I agree I like 0.25 (I believe thats what CNS spits out). Anything tighter looks fabricated -- Yuri Pompeu

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Simulated annealing composite omit map conversion
by Yuri 09 Oct '11

09 Oct '11

Hello Everyone, I am calculating an SA. composite omit map to show active site density. It looks like the output format is mtz coefficients. How can I get it to ccp4 or .xplor format for PyMol? Thanks -- Yuri Pompeu

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Educative Tool Idea
by Yuri 07 Oct '11

07 Oct '11

Hello Developers, This may be a silly idea after all, nonetheless: Would it be possible (worhtwhile) to have a tool that lets the user input a molecule of a certain type (probably rather small size, i.e, an amino acid or cofactor), and then input a space group. Phenix could then generate a relection file that would be displayed using either data2d or 3d viewer. Obviously there are many other factors to be considered but just an idea... -- Yuri Pompeu

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Occupancy refinement issue
by AFL 07 Oct '11

07 Oct '11

Dear All, I would like to refine the occupancy of _all_ components together for the following system: - free LYS (chain A and resname LYS) - PLP-LYS complex (chain A and resname LLP) - PLP-GLU complex (chian D and resname PPE) The LYS and LLP are defined as alternative conformations. What I've tried so far is: - just phenix.refine without any additional constraints and the result is occupancy refinement of LYS vs. LLP and separately refined PPE. - constrained_group { selection = chain A and resseq 90 # position of LYS, LLP selection = chain C and resseq 1 # PPE } Result is occupancy refinement of LYS+LLP vs. PPE and total mess in the active site (=ligands moved to new positions far away from where they should be). - constrained_group { selection = chain A and resname LYS # ALYS, BLLP doesn't work selection = chain A and resname LLP selection = chain C and resname PPE } Results in occupancy refinement of LYS vs. PPE and the LLP occupancy is set to 0.00. So, the big question is: - is what I'm trying to do doable at all? - what would be the right way to do it? I will appreciate all and any suggestions on how to proceed. Regards, Andrzej Lyskowski -- alnyds(a)gmail.com e-mail home

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PHENIX atom selection language
by Jianghai Zhu 07 Oct '11

07 Oct '11

Hi, Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks. -- Jianghai

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Fwd: Really good stats... Unreal!??
by Yuri 05 Oct '11

05 Oct '11

Hi everyone, So I am done refining a structure with around 760 residues in the model to a resolution of 2.29A. Rwork 0.18 Rfree 0.24 RMSD angle 1.1 Bond 0.008, clashscore 28. As a I last round I ran optmize_weights and got some interesting numbers. Rwork 0.17 Rfree 0.23 RMSD Angle 0.68! Bond 0.003! clashscore 10.2 I dont know how real these are. That would make this a new pdb record for tight geometry!!! Any ideas? Best, -- Yuri Pompeu -- Yuri Pompeu

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local refinement of target weights?
by Yarrow Madrona 04 Oct '11

04 Oct '11

Hello, I am wondering if there is a way to restrain geometry target weights for a ligand seperate from the rest of the molecule. I would like to impose higher restraints for the ligand than that of the protein in the same refinement run. Thanks for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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combinding two CIF's and creating links in elbow
by Yarrow Madrona 04 Oct '11

04 Oct '11

Hello, 1. I have a question on creating links using elbow. I have a CIF of NO and I want to define a chemical link between NO and Fe of a HEME group. I need to input the geometry as NO is acting as a metal ligand. I really don't know where to begin. Any help would be greatly appreciated. 2. Is there a quick way of combining CIF files into one large file without a lot of copy and pasting? Thank you. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Phenix version 1.7.2 released
by Paul Adams 01 Oct '11

01 Oct '11

The Phenix developers are pleased to announce that version 1.7.2 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - phenix.data_viewer added under Reflection Tools - New GUIs: HySS, phenix.cut_out_density, phenix.reciprocal_space_arrays General: ======== - New commands: phenix.cut_out_density, phenix.data_viewer, phenix.morph_model - Default map output format changed to CCP4 - Native support for CIF-format reflection files (e.g. from PDB) in many commands and GUI Refinement: =========== - New Xray/restraints weight optimization. Keywords optimize_wxc and optimize_wxu replaced with optimize_xyz_weight and optimize_adp_weight, respectively. - Grid searches parallelized: use 'nproc' parameter to set number of CPUs to use - this affects bulk solvent mask optimization, and XYZ and ADP weight optimization (in addition to TLS identification) - can reduce runtime by 75% or more depending on settings (see manual for details) - Modified non-bonded parameters resulting in improved geometry, especially at low resolution - Rigid-body refinement mode defaults to grouping by chain - Printout of validation statistics during coordinate refinement - Bug fix in phase-combined map calculation results in significantly improved maps - Bug fix in X-ray/ADP restraints weight calculation results in smaller B-factors deviations for bonded atoms - Experimental feature (still in testing): - Torsion-space NCS (ncs.type=torsion), automatic parameterization, similar to reference model restraints - Uses top-out potential to allow deviations between NCS related atoms New commands: ============= - phenix.cut_out_density: - carve out a region from map coefficients (MTZ file) - density may be specified as a sphere, a box, or masked around a PDB file - phenix.data_viewer: - visualization of reciprocal-space reflection data - 3D OpenGL view of all data, or 2D view of planes (pseudo-precession photograph) - phenix.morph_model: - Use after molecular replacement to improve model for rebuilding - Morphs model to match a prime-and-switch map Molecular Replacement: ====================== - Phaser (and AutoMR wizard): - significant speedup of fast rotation function Miscellaneous: ============== - phenix.reel: - better integration with main GUI, especially eLBOW - phenix.fobs_minus_fobs_map: - option to disable strict unit cell isomorphism check - phenix.ramalyze: - optional output of PNG images of Ramachandran plots; add --plot to command line arguments - phenix.fetch_pdb: - new flags: --all fetches PDB, CIF, and FASTA files simultaneously --mtz runs phenix.cif_as_mtz on downloaded CIF file For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). 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. -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 Head, Berkeley Center for Structural Biology Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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