- phenixbb - phenix-online.org

Phenix "hangs" on a Mac?
by Joseph Noel 22 Jul '13

22 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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Registration open: "The Future of Microfocus Protein Crystallography"
by Marjolein Thunnissen 22 Jul '13

22 Jul '13

Dear all, I would like to remind you on a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White, Luca Jovine and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting, but there is no requirement to be a user of the facility and all that are interested are welcome . Registration is through the user meeting website: https://indico.maxlab.lu.se/indico/conferenceDisplay.py?confId=0 . The registration fees are 2000 SEK for academics and 700 SEK for junior scientists. Registration fees include all lunches and the conference dinner. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen 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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Fo-Fo map
by Xiang Li 22 Jul '13

22 Jul '13

Hi everyone, I am working on two datasets of the similar crystal design. In one of the datasets, there is an extra guest protein (might be considered as a ligand) docked in one unit cell. The two crystals have very similar unit cell size and same symmetry. I want to calculate the Fo-Fo map to see whether I could figure out where the protein is. But I got error says the symmetry of the two datasets are not the same. I have never used the "isomorphous difference map" in GUI before. Can anyone help me to figure out where I did wrong please? I have attached the mtz file that I want to compare. Btw, if the protein is not very rigidly linked with the crystal framework (~2 free residues linkage), am I supposed to see the density of the protein? Or are there any better ways for me to identify the protein? Thanks for your kind help! Sincerely, Xiang

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ADP refinement of cysteinesulfonic acid
by Phillip Steindel 16 Jul '13

16 Jul '13

Hi all- I have a 1.5 Angstrom structure with two cysteines that appear to have oxidized to cysteinesulfonic acid (OCS). I replaced the cysteines in coot, then ran refine with individual and anisotropic ADPs, but the ADPs don't appear to be refining for those residues. The hydrogens are all at 24,and the non-hydrogens are all at 20. I'm running 1.8.2-1309. Thanks, Phillip Steindel Theobald Lab Brandeis University

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cis peptide question
by Edward A. Berry 16 Jul '13

16 Jul '13

I have a cis-peptide in my structure. Phenix recognizes it and .geo file shows this is restrained to 0*: dihedral pdb=" CA ALA A 401 " pdb=" C ALA A 401 " pdb=" N SER A 402 " pdb=" CA SER A 402 " ideal model delta harmonic sigma weight residual 0.00 -1.58 1.58 0 5.00e+00 4.00e-02 1.00e-01 However in statistics printed with the output pdb, I have at least one dihedral that is flagged as off by about 180*: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 DIHEDRAL : 12.902 168.987 3277 ^^^^^^^ Could this be my cis peptide, or do I have a really bad dihedral somewhere else?

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How do I turn off sidechain rotamer fitting?
by Owen Pornillos 15 Jul '13

15 Jul '13

I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature? Many thanks, Owen

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Kicked difference maps
by Ho Leung Ng 13 Jul '13

13 Jul '13

Hi, I am finding that features in kicked difference maps (mFo-DFc) have very different scaling compared to the standard difference maps. For example, a blob that appears in the standard map at 3 sigma might not appear in the kicked map until 5.5 sigma. Is this correct functioning? In contrast, features in the kicked and standard 2mFo-DFc maps are comparable in scale. Thank you, Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry hng(a)hawaii.edu

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problem with alternate conformations
by George Phillips 11 Jul '13

11 Jul '13

I am trying to adapt my old CNS scripts to to multiple conformer refinements in Phenix, i.e. up to 20 copies of each entire chain. I seem to be OK with up to three copies of the whole chain, but when I try four or more I seem to be in an infinite loop in the 'reduce' phase of a refinement. 3 copies runs in less than hour, even with torsion simulated annealing, with four even overnight the program just runs 'reduce for hours and hours'. This happens on the standard release and development version 1422. Is there some way to turn off hydrogens as a work around? Test files available on request. : ) Thanks for any help! George George N. Phillips, Jr. Ralph and Dorothy Looney Professor Department of Biochemistry and Cell Biology Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 http://www.bioc.rice.edu/

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