- phenixbb - phenix-online.org

proteins sequence for phenix
by LISA 26 Jul '13

26 Jul '13

Dear All, Phenix will ask for the protein sequence when we create a new project. I try to solve my complex by the Autosol in phenix with proteins sequence. My complex contains 2 molecule A and 3 molecule B. How can I give the sequence in phenix? will it should be: >A .................................................................................................................. >B .............................................................................................................................. or >A .................................................................................................................. >A .................................................................................................................. >B .............................................................................................................................. >B .............................................................................................................................. >B .............................................................................................................................. Thank you. Lisa

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Re: [phenixbb] On Mac two separate installations?
by Joseph Noel 26 Jul '13

26 Jul '13

Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps! Also, following the protocol as outlined by Andy Karplus in his Science paper on data processing using data extending to CC1/2's near 0.2. Both together seem to really extend the resolution of my datasets and also improve refinement! ______________________________________________________________________________________ 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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Fwd: Course on “Structure and Function of Membrane Proteins- a multidisciplinary approach”
by Nathaniel Echols 26 Jul '13

26 Jul '13

---------- Forwarded message ---------- From: Jose Artur Brito <jbrito(a)itqb.unl.pt> To: phenixbb(a)phenix-online.org Date: Fri, 26 Jul 2013 15:58:01 +0100 Subject: Course on “Structure and Function of Membrane Proteins- a multidisciplinary approach” Dear colleagues, We would like to announce the Instruct-sponsored 4-day course “Structure and Function of Membrane Proteins- a multidisciplinary approach”, to be held at ITQB, Oeiras (nearby Lisbon), Portugal, from 5 to 8 November 2013. The course will address several techniques for the structural and functional characterization of membrane proteins, with special emphasis on Macromolecular Crystallography, Mass Spectrometry, Electron Microscopy and Nuclear Magnetic Ressonance. The information provided by each technique, their applications in biological systems, major benefits and limitations will be discussed. The course is organized with lectures in the mornings and interactive tutorials in the afternoons. In addition, the selected applicants are grouped and each group works on a case study (based on 2-3 papers covering techniques of interest and a questionnaire) and gives a presentation at the end of the course. The course is aimed primarily at PhD students, young Post-Doctoral researchers and others with research activities involving structural biology of membrane proteins. Participants will be limited to 20. Candidate selection will be based on a short CV, a motivation letter from the applicant, and a recommendation letter from the supervisor. Registration deadline is September 16, please send your application to membstruct2013(a)itqb.unl.pt . More information can be found at http://www.itqb.unl.pt/membstruct2013 The organizing commission, Margarida Archer (ITQB-UNL), Carlos Cordeiro (FC-UL) and José A. Brito (ITQB-UNL) -- ************************************************ * José Artur Brito, PhD * * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal * * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbrito(a)itqb.unl.pt * * URL: http://mx.itqb.unl.pt * ************************************************

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

25 Jul '13

Dear users, We are in the process of rearranging our server room and changing the way we do the nightly builds. One step of this will be retiring the bulky and ancient boxes which run Fedora 3, and standardizing on slightly more modern OSes. (Including Ubuntu-specific builds, as well as the usual Fedora/RedHat/CentOS base.) I know that some people have found that the Fedora 8 x86_64 build does *not* run properly on their systems, but the Fedora 3 build does. Could anyone who has firsthand experience with this please contact me off-list and tell me exactly which distribution and version you are running? We can't cover all possible combinations (sorry Gentoo users), but I'd like to get some idea what is still problematic. thanks, Nat

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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 24 Jul '13

24 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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