- phenixbb - phenix-online.org

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 04 Jul '10

04 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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Which is the better way to combine the dataset from different crystals?
by fn1＠rice.edu 01 Jul '10

01 Jul '10

Hi all, I have a question on how to combine two dataset from different crystal of the same protein. The first way I could think of is that, 1) Merge two dataset seperately; 2) Scale them to see whether they are consistent with each other enough as indicated by the R-factor; 3) If the R is low enough, say below 10 or 15%, then take the average for both the F and SIGF. The other way is that, 1) Take the unmerged file from MOSFLM, and reset their batch number; 2) Run SCALA to scale these two unmerged dataset at the same time. Could anyone tell which way is the better or the correct way? Thank you in advance! Alphar

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Reference for phenix.elbow
by Michael Hothorn 30 Jun '10

30 Jun '10

Hi, is there a reference for phenix.elbow? Thanks Michael

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NCS constraints in phenix
by Kenneth Verstraete 30 Jun '10

30 Jun '10

Dear all, I am working on a low resolution dataset (4.2 angstrom) of a multidomain complex. Using MR and density modification with NCS I obtained map in which I am extending/modifying my MR-models for the different domains. I tried to build the mainchain as a polyala model (extending on my MR-models) and then refined my new model in phenix.refine using torsion angle refinement. I have fourfold NCS and I think a this point it would be advantageous to use NCS-constraints instead of restraints. Is this possible in phenix? If I set the coordinate_sigma in de .def file to zero will this result in constrained NCS-refinement? ncs { restraint_group { reference=XXX selection=YYY coordinate_sigma=0.00 b_factor_weight=10 } Thank you very much for your advice, kind regards, Kenneth

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