July 2010 - phenixbb - phenix-online.org

phenix.maps kick maps: seed and error
by Alastair Fyfe 12 Jul '10

12 Jul '10

Hello, I have started using phenix.maps to calculate some kicked omit maps and had two questions: 1) is there a way to control parameters such as the initial random seed or number of kick iterations? Different runs with the same params and input files appear to give different map coefficient outputs. 2) after what appears to be a successful run on a pdb containing two rna chains and solvent atoms I (a) removed all non-RNA atoms and (b) moved all RNA atoms to corresponding symmetry locations within the ASU. No other changes were involved but I now receive the following python stack trace: Compute maps. Traceback (most recent call last): File "/home/afyfe/phenix/phenix-1. 6.1-357/cctbx_project/mmtbx/command_line/maps.py", line 192, in <module> run(args=sys.argv[1:]) File "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/command_line/maps.py", line 168, in run params = params.maps.map_coefficients) File "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/maps/__init__.py", line 295, in __init__ coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp) File "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/maps/__init__.py", line 257, in map_coefficients_from_fmodel average_maps = False).map_coeffs File "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/map_tools.py", line 73, in __init__ map_helper_obj = fmodel.map_calculation_helper() AttributeError: 'twin_model_manager' object has no attribute 'map_calculation_helper' thanks, Alastair

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solve won't run.
by alexander.singer＠utoronto.ca 09 Jul '10

09 Jul '10

Hi -- I installed phenix-installer-1.6-289-intel-linux-2.6.tar on my Fedora Core 5 linux partition and most things run -- but not solve (which I was first trying from autosolve). As recommened by the documentation, when I type phenix.solve, here's what I have --- [root@ausinger oth32_c]# phenix.solve binary=/usr/local/phenix-1.6-289/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=1862380800 /usr/local/phenix-1.6-289/build/intel-linux-2.6/solve_resolve/exe/solve: error w hile loading shared libraries: /usr/local/phenix-1.6-289/build/intel-linux-2.6/l ib/libimf.so: cannot restore segment prot after reloc: Permission denied Do you know what I can do about this? Thanks Alex -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

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Re: [phenixbb] solve won't work
by alexander.singer＠utoronto.ca 08 Jul '10

08 Jul '10

Tom -- what you recommended seemed to work -- phenix.solve doesn't crash out any more, and I'm just trying to see if I get a solution using autosol with my new dataset. Again, thanks and I'll let you know if I find any further problems. Alex -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

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Phenix auto-excluding some reflections
by Sam Stampfer 08 Jul '10

08 Jul '10

Hi, I'm in the process of depositing coordinates for a few structures and I noticed that the "number of unique reflections (observed)" is different in the "refinement statistics section" (108812) (read automatically from the phenix-refined pdb file) versus the "reflections" section (118749). The "cut- off sigma(F)" value is 0.12 (read automatically from the phenix-refined file). What criteria does phenix use to reject these ~10,000 reflections? Thanks! -Sam

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phenix-online.org web server issues on Friday?
by Ben Eisenbraun 06 Jul '10

06 Jul '10

Howdy PHENIXians, One of my users reported a "Error attempting to get current version list: HTTP Error 500: Internal Server Error" on Friday morning last week. Looking through the source, I see: phenix/phenix/utilities/check_version.py which seems to do a version lookup against: http://www.phenix-online.org/download/get_versions.cgi It would be good to set an explicit timeout on the urlopen so the GUI doesn't hang on network errors, web server blow ups, etc. AFAICT, urllib2 uses the default global timeout for the socket module, but socket has no default timeout, so calls to a broken web server can hang your python program. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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TLS refinement in phenix
by Mirage Singh Baliyan 06 Jul '10

06 Jul '10

Dear all, I am refining a 2.25 A structure in phenix using TLS parameters. In the generated PDB there is one ANISOU record along with the ATOM record. I am not understanding this. can anybody help me about this Regards Mirage singh Protein crystallography Laboratory IMTECH (IMTECH is a research establishment of CSIR, india) Chandigarh

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Phaser heavy atom sites - question
by Peter Grey 06 Jul '10

06 Jul '10

Dear all, Phaser SAD module found roughly 200 sites of my heavy atom. Phaser writes the location of the sites within an ASU. I am looking for a tool that can transform these sites to the corresponding sites within and just around my model. Thank you in advance for any suggestions, Peter.

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hi
by intekhab alam 06 Jul '10

06 Jul '10

I am a new user to phenix and have just started with Phenix.refine using GUI. I want to fix the co-ordinate of ligand atoms in my structure and then refine it. can anyone help me to do that in phenix GUI. Thanks in advance Regards INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Computational Crystallography Newsletter - Issue 1
by Paul Adams 05 Jul '10

05 Jul '10

Dear Colleagues, I am pleased to announce the publication of the first issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ It features articles, meeting announcements and reports, information on research and other items of interest to crystallographers and users of crystallographic software. The target audience is structural biologists including both students and experts. Anyone interested in publishing articles or other items in the newsletter is encouraged to contact the editor at any time. Submission of text by email using the word-processing templates available online is requested. Cheers, Paul -- 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: 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: Marian Harris [ MSHarris(a)lbl.gov ] [ 1-510-486-6886 ] --

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queueing system support in GUI
by Nathaniel Echols 05 Jul '10

05 Jul '10

The most recent nightly build (dev-457) adds the ability to run jobs on Sun Grid Engine. To activate this feature, go to Preferences->Processes and click "Activate queueing system support"; this will add a queue job option to the menu that appears when you click the Run button. I'm hoping that the default command-line arguments I picked are suitable for most environments. Obviously the filesystem that you run jobs on must be visible both to the host machine and to the machines in the queueing system. The same PHENIX installation must also be accessible from both. You need to be able to submit jobs from the machine that you're running the GUI on. (FYI, you could be running everything on a single multi-core computer - there's no reason why this has to be done on a cluster, but that's what I'm testing it on.) You can view the current queue status from the main GUI via "Show queue status" in the utilities menu. (You can't actually delete jobs from there yet, despite the misleading button that I forgot to remove.) Some caveats: - This should, in theory, run on heterogeneous clusters, but I haven't tried this because all of our systems are 64-bit Linux. - I haven't tried it on Mac either. - There will probably be some weirdness associated with closing the GUI and resuming jobs while still running, especially if you try to abort them. - The built-in parallelization of AutoBuild and the ligand identification program will not play nice with the queueing system when using this mechanism (this is really a defect in queueing systems, not AutoBuild). I think it will be relatively easy to fix this, but for now, you're better off using a single multiprocessor machine for parallel AutoBuild runs in the GUI. - If the queueing system or remote host crashes, the GUI will still think the job is running. Those of you who are interested in using this, please let me know how it works and what features are missing. As always, I fully expect that this will break on some setups. thanks, Nat

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