- phenixbb - phenix-online.org

GUI display items
by Luca Pellegrini 10 Mar '13

10 Mar '13

Hello, Is there a way to change/select the column items displayed in the PHENIX home window, under the 'Job history' tab? At the moment, mine shows: ID/Program/Date/Job title or directory/R-free. I would like to add things like the Overall score from MolProbity etc. I looked under Preferences but couldn't find anything. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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fwd: EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013
by Nathaniel Echols 09 Mar '13

09 Mar '13

(Note that the registration deadline is tomorrow.) ---------- Forwarded message ---------- From: Daniele de Sanctis <desancti(a)esrf.fr> To: phenixbb(a)phenix-online.org Date: Sat, 9 Mar 2013 12:51:54 +0100 Subject: EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013 DEADLINE Tomorrow COURSE ANNOUNCEMENT EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013 The EMBO 2013 Practical Course on Exploiting Anomalous Scattering in Macromolecular Structure Determination will be hosted by the ESRF in Grenoble, France from 10 to 14, June 2013. The course aims to impart the theoretical and practical basis for the 3-dimensional structure determination of bio-macromolecules using Anomalous Dispersion techniques (SAD & MAD) to young scientists who intend to apply these methods in macromolecular crystallography. Through a series of lectures, software demonstrations, practicals on the ESRF beamlines and tutorials, participants will get insights into all aspects of the structure determination process including beamline instrumentation, data collection and processing, heavy atom substructure determination, phasing and model building. There will also be sessions focusing on automated structure solution procedures and newer methods. Additional sessions will include presentations of distinguished structures solved with these techniques. The number of participants is limited to 20 and the deadline for application is March 10th, 2013. Additional information, course programme and instructions to apply to the course can be found in the course webpages: http://events.embo.org/13-crystallography/ Confirmed invited speakers include: Andreas Bracher, Kay Diederichs, Rita Giordano, Adrian Goldman, Wolfgang Kabsch, Gordon Leonard, Airlie McCoy, Sean McSweeney, Christoph Müller-Dieckmann, Max Nanao, Alexander Popov, Harry Powell, Thomas Terwilliger, Andrew Thompson, Isabel Uson, Clemens Vonhrein -- ἀρετή --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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map woes from refine
by Machius, Mischa Christian 08 Mar '13

08 Mar '13

Y'all, Recently, I've run into an issue with the maps from refine. All during the refinement cycles, the autoupdated maps in the associated coot window look great as refinement progresses. However, the final maps look horrible; completely chopped up. It's not a matter of contouring levels; it's essentially unrecognizable, and phenix acknowledges that by stating very low correlation coefficients at the end of the log file. I have downloaded the latest builds in an attempt to address B-value issues that were recently discussed and that I am (still) struggling with. The map issue happens with all of them. Is it possible that there is some crossfire from different versions, or any other reason? Any help appreciated. Cheers, MM

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selection of different residue ranges for a NCS group
by Andres PALENCIA 07 Mar '13

07 Mar '13

Dear All, I am trying to select different regions of the same protein to be included in the same NCS group before refinement. This correspond to the core of a protein. Additionally, I would define other NCS groups for external domains. I have 4 protein/RNA complexes in the asu, P1. Here are the residue ranges for the NCS group corresponding to the core of the protein (invariant): Chain A and resseq: 1:156, 188-227, 413:568, 629:794 this should be the reference group, to match the same region in the other 3 monomers (C, E. G). Other NCS groups will include the RNA, as well as other external domains: Chain B and resseq: 1: 87 This is the RNA molecule, that should match the other 3 monomers (D, F, H) Chain A resseq: 157:187 this is a external domain, to match the other protein monomer (C, E, G) and so on.... for other external domain I have seen that there is the possibility to use user-defined NCS groups, by using: * ncs_groups.params * or modifying the GUI by editing the atom selection For the external domains I think is easy as the syntax is only one line, however for the core of the protein I do not manage to select properly the different residue ranges. Could anybody please help on that? what would be the easiest way to do that? Can I for example creat a ncs_groups.params file and add it to phenix.refine in the GUI? Thanks in advance, Andres

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map scaling: sigma or volume scaled
by Edward A. Berry 07 Mar '13

07 Mar '13

map scaling can be defined: sigma or volume scaled Maybe another dumb question, but what is volume scaling? For 2mFo-DFc and mFo-DFc maps. Thanks, Ed

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quick clashlist or molprobity in batch mode
by jan 06 Mar '13

06 Mar '13

Hi all, I want to analyze a whole bunch of structures with molprobity, and I am looking for a convenient way to do this. phenix.quick_clashlist seems to be a handy tool. However, when I use the following command line: "phenix.quick_clashlist model=mypdb.pdb" ... the output tells me: # run_clashlist # # Run reduce and molprobity # type phenix.run_clashlist: --help for help Parameters used: run_clashlist { model = "4iuj.pdb" build = True summary_file = None output_file = None temp_dir = None remove_temp_dir = None verbose = False raise_sorry = False debug = False dry_run = True } ************************************************ 'str' object has no attribute '_anchor' ************************************************ Any ideas what I need to do differently? thanks, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

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Using Phenix Refine for Hypothetical Models
by Sam Stampfer 06 Mar '13

06 Mar '13

Dear Phenix Community, Is it possible to use phenix.refine to do simulated annealing and energy minimization of a hypothetical model? I am currently using pyrosetta relax for minimization; however, my hypothetical model is based on a homologous protein whose structure is a crystallographic trimer. I would like to preserve my model's symmetry, which I know is possible in phenix.refine but not in pyrosetta (the symmetry controls are only supported in regular rosetta, as far as I know). Is there a way to have phenix ignore x-ray data and just do energy minimization functions? How would I go about doing that? Would I need a file containing fake/dummy x-ray data? Thanks for your help! -Sam Stampfer

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Fwd: FINAL REMINDER: ALS Call for General User Proposals - DEADLINE March 6 2013
by Banumathi Sankaran 05 Mar '13

05 Mar '13

Dear Users, I am forwarding the reminder mail from ALS to submit your proposal for the CC time and general user time at ALS. Please submit your proposals before time. Thanks Banu FINAL REMINDER: CALL FOR GENERAL USER PROPOSALS AT THE ALS The User Services Office is accepting General User Proposals from scientists who wish to conduct research at the ALS in the next cycle. PROPOSAL SUBMISSION DEADLINE cycle: 2013-2 August-December Deadline: March 6, 2013 NEW PROPOSALS Please follow the instructions for proposal submission at: http://www-als.lbl.gov/index.php/user-information/user-guide/58.html BEAM TIME REQUEST for an ACTIVE PROPOSAL Proposals remain active for two years (up to four cycles), but beam time is only allocated if a beamtime request is made each cycle. After two years the proposal expires and a new proposal must be submitted. If you have an eligible active proposal you will already have received an email from us which includes your login number and password. PUBLICATION REMINDER The proposal form now includes a section on publications from previous ALS work. Please make sure your publications are entered into our database: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PublicationSearch.shtml/Initialize If you have questions, please feel free to contact me. Cheers, Clyde Lewis Proposal Coordinator ALS

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Memory and CPU usage
by Jon Agirre 05 Mar '13

05 Mar '13

Dear community, I'm planning on buying a new macbook for my first abroad postdoc venture, and I'm currently trying decide what amount of RAM & CPU to choose. My question is a little bit intricate: is there any rule of thumb to estimate the needed RAM versus the number of input atoms for any particular refinement type? I'm planning on tackling some big (18,000 residues/asu) refinements but I don't have any estimation as to how many GBs of RAM they might require. The maximum amount of RAM I can install is 16GB, but it is a non-standard configuration that might void Apple's warranty. About the CPU: how scalable are typical phenix processes? Would it be sensible to invest in a quad-core machine with HT? In this particular case, and since HT would present 8 logical cores, would I get any speed up from launching phenix tasks configured for 8 processors instead of 4? Thanks in advance! Jon

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Unusually low B factors with phenix 1.8, but not with phenix 1.7 (data set has ice rings)
by Oliv Eidam 05 Mar '13

05 Mar '13

Hi, I would like to continue the B-factor discussion started by Demetres D. Leonidas on Nov 2, 2012 on CCP4BB: http://www.mail-archive.com/[email protected]/msg29012.html I make the same observations like Demetres and Mingzhu Wang: unusually low B-factors when refining with Phenix 1.8-1069 and 1.8.1-1168, but not with Phenix 1.7.1-743. In numbers: the average B-factor is 10 A2 but it should be 20 A2 (based on Wilson B and similar structures). A few atoms (~20) have Bf = 0.00. The following is important: I refined dozens of similar structures without that problem and I observe this phenomenon only for a single data set. That specific data set is different because 1) I excluded regions with ice rings in XDS and 2) I limited the resolution to 2.28 Angstroem, although the crystal diffracted to ~1.8 Angstroem. While the preparation of the data set might be questionable in itself, I would prefer that this would not be the topic of this thread. My questions are: What can I do to refine my structure with Phenix 1.8.X using this truncated data set? What causes the difference in average B-factor values between Phenix 1.7 and 1.8 for this data set? Your advice is much appreciated. Oliv On 11/04/12 19:21, mingzhu wang wrote: > Pavel, > > 1.8.1-1168 also has this problem. > > I found this problem existed with some dataset, but not all dataset. > > 1.8.1 give better map, so I built model with 1.8.1 map and go back to > 1.7.3 before I deposit the structure to PDB. > > When I compared the B factor from 1.8.x and 1.7.3, I found > B(1.7.3)=B(1.8.x)+Boverall(1.8.x). Perhaps this is the problem. > > > > 2012/11/3, Pavel Afonine<pafonine(a)gmail.com>: >> Joao, >> >> I am using the latest version of phenix 1.8.1-1168 >> >> >> 1.8.1-1168 should not have that "problem". >> >> If you suspect there is still a problem, you can send me the data and model >> files off list, explain what exactly the problem is, and I will have a look >> right away. >> >> FYI: there is Phenix mailing list for Phenix-specific questions, where I >> can also explain in great details the behavior with the B-factors you >> observe. >> >> All the best, >> Pavel >> -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email:[email protected]

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