- phenixbb - phenix-online.org

MemoryError
by Yingjie Zhou 18 Aug '08

18 Aug '08

2 2

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. --

1 0

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/

2 1

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. > >

1 0

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

2 1

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

1 0

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

1 0

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

1 0

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

4 5

phenix.reduce
by Mayer, Mark (NIH/NICHD) [E] 13 Aug '08

13 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

2 1