- phenixbb - phenix-online.org

Refinement using a homolog as a reference
by Joshi, Amar (Dr.) 25 Jul '13

25 Jul '13

Hi, I am refining ligand-protein complexes at 3.2Å dataset with a human protein. My Rfree is ~0.34 but my ramachandran stats are concerning me: 85% favoured, 4.5% disallowed. The structure of a yeast homolog has been deposited at 2.4Å resolution. The yeast structure contains additional loops but is ~55% identical to the human protein. The overall conformation between the homologs is very similar. Can I use this as a reference model? Should I prune the reference model? Will different numbering schemes affect the refinement? Many thanks, Amar

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Re: [phenixbb] Linux distribution question: who needs the FC3 build?
by Nathaniel Echols 25 Jul '13

25 Jul '13

On Wed, Jul 24, 2013 at 2:56 PM, Edward A. Berry <BerryE(a)upstate.edu> wrote: > Would that be the end of support for 32-bit linux? Or would you build > i686 version on a later version? (Or is it possible to run 64 bit > executable on 32- bit operating systems with some kind of compatibility > libraries and 64-bit capable hardware?) > > I have one Fc8 32 bit machine which I don't want to upgrade, but I don't > really need to run phenix on it. Just to clarify: we will continue distributing 32-bit Linux indefinitely (although probably on fewer platforms than 64-bit), and we will at least support Fedora 8 at a minimum for a while, since our most important development system is still running it. The question is really related to how ancient a distribution we need to support, and what scenarios are especially difficult for binary cross-compatibility. -Nat

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calculate map from ensemble refinement
by Bard, Joel 23 Jul '13

23 Jul '13

Hi- I ran phenix.ensemble refinement which worked very nicely but crashed during map output. I think this was my fault for using a parameter file that had map_type = None (I didn't look and assumed the default was reasonable). I would like to calculate maps after the fact. Is there a way to run the map calculation on the output ensemble pdb file and reflection data? I tried phenix.maps which choked on the huge ensemble. Thanks, Joel

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Group ADP refinement
by joseph Lyons 23 Jul '13

23 Jul '13

Dear phenixbb. I am currently running phenix 1.8.2-1309. My goal is to use group ADP with 2 b-factors per residue for the protein and individual b-factors for solvent. However, this does not seem to be working even though the system seems to recognise what I want to do. The refinement output gives what looks like individual b-factor refinement... ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4048 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 127 aniso = 0) group_adp = True (3921 atoms in 967 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False In troubleshooting it appears that with Group ADP with 2 b-factors per residue, the solvent B-factors are not being refined, i.e., remaining at the Wilson B that I set previously. For Group ADP with 1 b-factors per residue - everything appears to refine OK. Any help would be greatly appreciated, Regards, Joe

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Re: [phenixbb] How do I turn off sidechain rotamer fitting? (Pavel Afonine)
by Joseph Noel 23 Jul '13

23 Jul '13

Dear Pavel, To clarify, in the latest nightly build, 1435, do you have to click on real space refinement to carry out side chain rotamer fitting? If you just refine xyz I assume side chain rotamer fitting is not enabled, correct? Joe Noel ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Re: [phenixbb] Phenix "hangs" on a Mac?
by Joseph Noel 23 Jul '13

23 Jul '13

Hi Nat, Will replicate and send you the information. Its unrelated to Ramachandran restraints as it occurs intermittantly when doing just regular tasks. I can always tell early as it never seems to get past the first steps of the refinement protocol - in essence - it never starts xyz refinement. Just sits there. I abort and restart and it then goes fine. I'm running Mac OSX 10.8.4 Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Post-doc position for SAXS at the MAX IV Laboratory
by Marjolein Thunnissen 23 Jul '13

23 Jul '13

The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow to strengthen the biological SAXS environment at the current SAXS beam line. The position will be for two years and is embedded in the BIOSTRUCT-X EU program. Full information of the position is available at: http://admin.lu.se/o.o.i.s?id=22598&Dnr=554436&Type=E as well as who to contact for more information. Information about the MAX IV laboratory can be obtained at www.maxlab.lu.se<http://www.maxlab.lu.se> . best regards Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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Phenix "hangs" on a Mac?
by Joseph Noel 23 Jul '13

23 Jul '13

Has anyone had a problem when using Phenix refine through the GUI on a Mac wherein the program after hitting Run locally starts but then hangs without proceeding? Seems to happen to me about one out of five times I run refine and always hangs when I experiment with ramachandran restraints for only a portion of the polypeptide chain. I've tried letting things alone for several hours and nothing happens. I can abort and then often resubmit and it then runs fine (except for rama restraints). I've found this happens with both nightly builds and stable releases. I am currently running the latest nightly build 1439. ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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On Mac two separate installations?
by Joseph Noel 22 Jul '13

22 Jul '13

Does one have to install both the GUI and command line installers on a Mac if one wants to have the option of running using the command line (for command line only options in nightly builds) and the GUI? ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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mr_rosetta pause & resume
by Karolina Michalska 22 Jul '13

22 Jul '13

Hello everybody, Is there a way to pause an mr_rosetta run and resume it with a different number of processors? Thanks, Karolina

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