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PHENIX atom selection language
by Jianghai Zhu 06 Oct '11

06 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 30 Sep '11

30 Sep '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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Twinned Refinement in P 1 21 1
by Yuri 29 Sep '11

29 Sep '11

I dont see spcgrp number 20 on here? Should I be concerned? >>> Unit cell: (44.767, 130.64, 88.33, 90, 104.6, 90) Space group: P 1 (No. 1) Angular tolerance: 5.000 degrees Similar symmetries ================== Symmetry in minimum-lengths cell: C m m m (x+y,2*y,z) (No. 65) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.36, 130.64, 90, 90, 104.674) Conventional setting: C m m m (No. 65) Unit cell: (44.767, 170.956, 130.64, 90, 90, 90) Change of basis: x-1/2*z,1/2*z,-y Inverse: x+y,-z,2*y Maximal angular difference: 0.079 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x-y,2*x,z) (No. 12) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.36, 130.64, 90, 90, 104.674) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (170.956, 44.767, 130.64, 90, 90, 90) Change of basis: 1/2*z,-x+1/2*z,-y Inverse: x-y,-z,2*x Maximal angular difference: 0.079 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x+y,2*y,z) (No. 12) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.36, 130.64, 90, 90, 104.674) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (44.767, 170.956, 130.64, 90, 90, 90) Change of basis: x-1/2*z,1/2*z,-y Inverse: x+y,-z,2*y Maximal angular difference: 0.079 degrees Symmetry in minimum-lengths cell: P 1 1 2/m (No. 10) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Conventional setting: P 1 2/m 1 (No. 10) Unit cell: (44.767, 130.64, 88.33, 90, 104.6, 90) Change of basis: x,y,z Inverse: x,y,z Maximal angular difference: 0.000 degrees Symmetry in minimum-lengths cell: P -1 (No. 2) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Conventional setting: P -1 (No. 2) Unit cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Change of basis: x,z,-y Inverse: x,-z,y Maximal angular difference: 0.000 degrees -- Yuri Pompeu

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Twin Refinement in P 1 21 1
by Yuri 27 Sep '11

27 Sep '11

So in other words, if I input the reflection and the space group as P 1 21 1 (lower symmetry vs the initially attempted C 2 2 21), and I specified the operator in the refinement parameters I should be ok, right? Thank you -- Yuri Pompeu

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Twin Refinement in P 1 21 1
by Yuri 27 Sep '11

27 Sep '11

Hello everyone, I have a twinned data set with PM twin operator h,-k,-h-l I was able to input the twin law into the refinement parameters, however I do not see a place that asks me for the law when generating the Rfree flags. Could someone point me in the right direction? Best, -- Yuri Pompeu

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renaming an holo PDB after the alo one
by Francois Berenger 27 Sep '11

27 Sep '11

Hello, I have one bound complexe (a ligand + a protein in holo conformation). I also have the apo structure for a very similar protein. Is there a tool to create a new PDB, whose coordinates are taken from the holo structure but residue names and numbers are taken from the alo structure (by looking at the corresponding residues in the output of a sequence alignment program)? I thought about doing a script using clustalw for the alignment part, but the task seems not trivial. Thanks a lot, Francois.

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real space residuals
by Bradley Hintze 26 Sep '11

26 Sep '11

Hey phenix, I see a util for real space correlation. Real space residuals are slightly different. Is the a tool to calculate RSR in phenix? -- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

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