- phenixbb - phenix-online.org

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

11 Oct '11

The figures are good illustration of what seems to be the consensus: Finely sampled maps can represent the best mathematical approximation of the continuous electron density function. The weirdness I referred to probably has more to do with what Nathaniel alluded to previously. The fact that our eyes get so used to staring at coarse pointy density - caused by the default grid of building programs (in the case of "on the fly" map generation from coefficients). That of course can be changed if one changes the sampling rate and get their eyes used to the new look. that I suppose would become your new norm. -- Yuri Pompeu

1 0

MR_Rosetta and dimer of heterodimer
by Morten Grøftehauge 11 Oct '11

11 Oct '11

Hi everybody, I'm trying to phase a dimer of a heterodimer of a large, ~700aa, and small, ~150aa, component. The only good search model according to HHpred covers the first 500aa of the large component. So I am wondering whether I should add the 150aa to the end of the sequence file and add them to the fragment files in order for phenix.mr_rosetta to do density modification correctly? Or does this not matter at all? According to HHpred and others the last 200aa are beta sheets, probably a a beta sandwich or two, and the 150aa component consists of helical elements but that is as close as it really gets. Cheers, Morten

2 1

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

11 Oct '11

hi Nathaniel, Thats simple enough... Do I have any control over grid ( make a tighter looking mesh for publication) -- Yuri Pompeu

8 9

Phenix not reading my sca files
by Scott Classen 10 Oct '11

10 Oct '11

Why? Error is: Unknown file format for file /home/me/phenix/autosol/s4_peak.sca Unknown file format for file /home/me/phenix/autosol/s4_infl.sca Unknown file format for file /home/me/phenix/autosol/s4_rem.sca this also does not work: phenix.reflection_file_converter s4_peak.sca --mtz . error is: file_name: s4_peak.sca file_type: None No reflection data found in input file. Please advise. Thanks, Scott Classen

2 5

Phenix file organization
by R.M. Garavito 10 Oct '11

10 Oct '11

To the Phenix gurus, I am in the midst of reorganizing our little Mac computer cluster, and will have a mixed collection of machines with OS 10.6.8 or 10.7.1. While the reorganization is going fine for the most part, I am having a little trouble getting Phenix to work on one machine. The problem is integrating a machine (a MacPro) into the cluster with users having different UIDs from their NIS accounts on the rest of the cluster. Thus, the NIS UID leads to not only a different UID for the user, but a different account (and therefore a different "home" directory) name. Simply changing ownership of the user's directories and files globally in OS 10.6.8 leads to Phenix choking at some stage when used under the NIS UID, but without an informative error message. Things go on fine when used under the old local UID and user name. So my question is does Phenix store the absolute paths in its various project indices? Any suggestions would be helpful. Thanks, Michael **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu ****************************************************************

2 1

Simulated annealing composite omit map conversion
by Yuri 10 Oct '11

10 Oct '11

"Fabricated" was probably a poorly chosen word. That implies made up data. I agree, I dont think cahnging the grid spacing would "introduce" unreal data to the maps... I just meant that it looks a little weird to have overly smooth mesh for a low res map... -- Yuri Pompeu

1 0

Computing Robs vs Rcalc for twinned data with xtriage
by Pietro Roversi 10 Oct '11

10 Oct '11

Dear all, I am trying to run phenix.xtriage to compute Robs vs Rcalc for twinned data (from A. A. Lebedev, A. A. Vagin and G. N. Murshudov Intensity statistics in twinned crystals with examples from the PDB, Acta Crystallographica, D62, 83-95, (2006) My input: phenix.xtriage xray_data.file_name=$1.mtz xray_data.obs_labels="IMEAN, SIGIMEAN" xray_data.calc_labels="FCalc, PHICalc" xray_data.high_resolution=3.1 > phenix.xtriage.$$.log The FCalc, PHICalc columns (from CCP4-sfall) are in my mtzfile: 1 ASC -27 27 0 100.00 0.7 10.4 52.72 2.60 H H 2 NONE -90 90 0 100.00 0.7 34.2 52.72 2.60 H K 3 NONE 0 15 0 100.00 5.7 5.7 52.72 2.60 H L 4 NONE 0.0 19.0 0 100.00 9.50 9.50 52.72 2.60 I FreeR_flag 5 NONE -244.3 13664.9 0 100.00 467.59 469.74 52.72 2.60 J IMEAN 6 NONE 1.8 990.9 0 100.00 43.05 43.05 52.72 2.60 Q SIGIMEAN 7 NONE 16.2 1157.9 0 100.00 173.14 173.14 52.72 2.60 F F 8 NONE 1.7 51.3 0 100.00 12.91 12.91 52.72 2.60 Q SIGF 9 NONE 0.7 7827.1 0 100.00 257.63 257.63 52.72 2.60 F FCalc 10 NONE 0.0 360.0 0 100.00 180.24 180.24 52.72 2.60 P PHICalc and yet I get the error message: creamint:~/Projects/FactorI/Tetartohedral/P1/DataFiles> ~/Scripts/phenix_xtriage.csh AUTOMATIC_DEFAULT_free.klh_sfall1 Running phenix.xtriage No matching array: scaling.input.xray_data.calc_labels=FCalc, PHICalc Possible choices: AUTOMATIC_DEFAULT_free.klh_sfall1.mtz:IMEAN,SIGIMEAN AUTOMATIC_DEFAULT_free.klh_sfall1.mtz:F,SIGF Please use scaling.input.xray_data.calc_labels to specify an unambiguous substring of the target label. Sorry: No matching array: scaling.input.xray_data.calc_labels=FCalc, PHICalc

2 1

Automated Mg & K ions picking
by Kristen Eisenberg 10 Oct '11

10 Oct '11

Hi Hasan, yes, we plan to extend water picking procedure so it can identify single-atom ions, but no specific tool is available to use right now. You need to inspect waters (for example, a water with "too small" refined B-factor is likely to be a metal), and density peaks (phenix.refine may not place a water into a density peak if it is too different from what is expected for water). Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen

1 0

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

1 0

Re: [phenixbb] Simulated annealing composite omit map conversion
by Yuri 08 Oct '11

08 Oct '11

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

1 0

Simulated annealing composite omit map conversion
by Yuri 08 Oct '11

08 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

2 1

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

6 10

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

2 1

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

2 6

Fwd: Really good stats... Unreal!??
by Yuri 04 Oct '11

04 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

2 1

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

2 2

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

2 1

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 ] --

1 0

Twinned Refinement in P 1 21 1
by Yuri 28 Sep '11

28 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

3 2

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

2 1

Twin Refinement in P 1 21 1
by Yuri 26 Sep '11

26 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

2 1

renaming an holo PDB after the alo one
by Francois Berenger 26 Sep '11

26 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.

1 0

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

3 3

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

2 1

Pseudo-merohedral twinning refinement in C2, when beta = 94 degrees
by John Pak 21 Sep '11

21 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!

2 2