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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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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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map CC given a model and map coefficients
by Francis E Reyes 26 Sep '11

26 Sep '11

Hi all I'd like to compute a resid by resid and overall map CC between a set of coefficients I specify and a model. Any utils to get this to me quickly? phenix.model_vs_data doesn't seem to take in custom coefficients. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Pseudo-merohedral twinning refinement in C2, when beta = 94 degrees
by John Pak 22 Sep '11

22 Sep '11

Hi all, I currently have a dataset that scales well in C2. (a = 224,b = 129,c = 392. beta= 94.5 degrees). Previously, I had thought that these crystals were in P6322 (posted this a few months ago), but I've since grown better crystals, where the beta angle is now 94.5, and not close to 90.0. I'm reasonably confident with the scaling - however, it has always been really difficult to index these crystals in HKL2000. Like the previous crystals, this new C2 dataset looks like it might be perfectly twinned, based on Xtriage's L test. I've solved the structure by MR, and refined it to 3.0 angstroms to R=30%, Rfree=33%, but I am running out of things to fix. I'd like to perform twinning refinement, based on this Xtriage L test result. The problem is that Xtriage cannot find any pseudomerohedral twinning laws, likely because the beta angle is too far from 90 degrees?? For kicks and giggles, I started to enter arbitrary beta angles in Xtriage, and at a beta angle below 93.4, Xtriage can find two twinning laws (closer to 90 degrees, Xtriage can find 5 twin laws). Using "-1/2*h+3/2*k, 1/2*h+1/2*k, -l" in Phenix refine (the beta angle is still 94.5 degrees, I haven't changed this) results in the R and Rfree dropping a lot to 25.5 and 28.6, respectively. Used the same random seed as previous runs to generate the test set from the scalepack file, with the "use lattice symmetry to generate test set" flag enabled. The maps look a lot noisier. So my questions are: 1. Is this twinning refinement valid? I'm really thinking no - since the maps didn't improve. Suppose the maps didn't get worse though - would this twinning refinement then be valid? 2. How do I go about reindexing this dataset in I2? i.e. to see if the beta angle with this unit cell selection is closer to 90 degrees. Would this even help, with respect to pseudomerohedral twinning refinement? Thanks!

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Maps Bias
by Yuri 22 Sep '11

22 Sep '11

I was having a discussion with a friend about maps and model bias. Is the Fobs/PHImodel more biased than 2FOFCWT/PHI2FOFCWt? What about an omit region of these two? Thanks for any opinion on this -- Yuri Pompeu

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Ligand / Loop occupancy refinement
by Antony Oliver 19 Sep '11

19 Sep '11

Dear all, Apologies if this has been covered already in a previous post — but I can't find a suitable response in the archive. We have the following situation... We have soaked a ligand into an apo-crystal, collected diffraction data, and solved the structure. What is apparent from the electron density, is that the ligand isn't in the crystal at full occupancy, it's roughly about 70-80%. However, as the ligand binds, it causes a small conformation change in the active site of the protein, altering the position of around 4 amino acids. What I want to do, and can't quite get phenix.refine to do is the following... Refine the occupancy of the ligand (chain C resname LIG) with the "A" conformation of the active site residues (which should be the same, as they are mutually dependent) — and then refine the occupancy of the "B" conformation of the active site residues — which should all theoretically add up to a total of 1. Could anyone help me with how the occupancies / constrained_group parameters should be set up in this case? With thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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bulk solvent mask question
by Laurie Betts 16 Sep '11

16 Sep '11

I notice that during refinement of a MR solution for a protein (search model is 100% homologous to target), a very large ligand-binding cavity (as much as 20 A wide in some parts) in my protein gives weak positive difference density for a ligand soaked into the crystals, unless I turn off bulk solvent modeling. Then the fo-fc difference density is quite strong (2.6 Angstrom data). I think this is due to part of the cavity being included in bulk solvent? Can I edit the mask easily, or flag parts of the protein as NOT exposed to solvent? Thanks Laurie Betts

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Refinement with optimize weights
by Ankit Gupta 16 Sep '11

16 Sep '11

Hello Forum, I am using Phenix 1.7.1-743 to refine my structure. My R/Rfree values for a 2.5 A structure were 0.22/0.305. I used optimize weights along with TLS and the R/Rfree values improved to 0.23/0.29. I wanted to know what parameters should I use for subsequent refinement. I read on phenix bb that one needs to fix the wxc_scale and wxu_scale. Is this correct? What values should be used for these parameters after running optimize wxc/wxu weights. Is there any place where I can get starting values for my future refinement? Also, I would like to know what Fix X-ray/stereochemistry weight and Fix X-ray/ADP weights are for? Thanks for the help.

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Phenix.refine distorts geometry during rigid body refinement
by Ian Slaymaker 14 Sep '11

14 Sep '11

I am bringing a PDB refined in Refmac back to phenix.refine. After an initial rigid body refinement to compare numbers (one chain per group), the geometry (specifically the bond length rmsd) had surprisingly increased. Phenix.validate confirmed the Refmac (initial) geometry numbers and then afterwards confirmed the distorted geometry. What is strange is that when opened in COOT, the initial and final models are completely super imposed. REMARK Start: r_work = 0.3375 r_free = 0.3624 bonds = 0.006 angles = 0.768 REMARK Final: r_work = 0.3379 r_free = 0.3626 bonds = 0.145 angles = 1.019 can you help me figure out what is going on here? These are the final few refinements of a 4.1 A structure. Thanks, Ian

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Linux kernel version 3.0 detection
by Ben Eisenbraun 14 Sep '11

14 Sep '11

Hi, Robert Campbell at Queens pointed out to me that the "machine_type" script bundled with PHENIX doesn't understand the new version 3.0 linux kernel strings. He tweaked his local copy for testing purposes on a Debian testing machine, and just forcing the 3.0 version to use the 2.6 binaries worked: case "$KERNEL" in 2.4.*) kernel_version=2.4 ;; 2.6.*) kernel_version=2.6 ;; 3.0.*) kernel_version=2.6 ;; *) kernel_version="$KERNEL" ;; esac I haven't tested it myself. It looks like Fedora 16 and Ubuntu 11.10, both targeted for November releases, will be using the new 3.0 kernel. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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Multiple conformations of disulfide
by Matthew Merski 13 Sep '11

13 Sep '11

Hello, I am trying to refine a surface cys that is alkylated by beta-mercaptoethanol (BME). The BME appears to have two poses and I am having trouble with getting phenix to understand the restraints. When I give the BME two conformations I get the error: Sorry: No atom selected: "chain A and resname ABME and resid 165 and name S2" My link_params file looks like this: refinement.geometry_restraints.edits { drgA_selection1 = chain A and resname ABME and resid 165 and name S2 bond { action = *add atom_selection_1 = $drgA_selection1 atom_selection_2 = $cys215_selection distance_ideal = 2.05 sigma = 0.02 slack = None } Not calling it ABME of course results in a non-unique atom error. Thanks for your help. Matthew Merski UCSF Shoichet Group

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phenix.refine restraint
by Simon Kolstoe 12 Sep '11

12 Sep '11

Dear phenixbb, I'm trying to constrain a ligand-metal bond that is continuously getting altered by phenix.refine (my data's only 3.2A). I've added the following restraint but it just doesn't seem to be holding the bond length during refinement. Is there a different way of telling phenix.refine not to alter this distance? (I'm doing it all on the command line & by editing the .def file). refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name CA and chain X and resname CA and resseq 1 atom_selection_2 = name O1 and chain L and resname ROC and resseq 1 distance_ideal = 2.380000 sigma = 0.100 } } Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Centre for Amyloidosis & Acute Phase Proteins UCL Medical School Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

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phenix.refine and ice rings.
by Francis E Reyes 08 Sep '11

08 Sep '11

Hi phenixer's / developers. A quick question: Curious, how are spots that lie on ice rings dealt with? At which step? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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