- phenixbb - phenix-online.org

Header accuracy after only refining ligands
by Katherine Sippel 25 Aug '14

25 Aug '14

Hi all, I was trying to prep a structure for PDB deposition. All the protein atoms were good, but I needed to correct some ADP and ligand issues. I ran coordinate refinement only on the ligands and subsequent ADP refinement. Everything was good, except the RSMD values output are clearly only for the ligands. Now I am wondering which values in the header I can trust as far as deposition goes. I tried to do a workaround where I ran refine with 0 macrocycles to see if I could get the proper values, but obviously the bulk solvent is different and I get higher R values. I am wondering if I can run validation to get the correct RMSD values or if there are other header values that might have been affected by not refining all the coordinates? Cheers, Katherine -- "Nil illegitimo carborundum"* - *Didactylos

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DEN refinement
by marinabb phenix 25 Aug '14

25 Aug '14

Dear all, I am trying to use DEN refinement as implemented in the Phenix-1.9 release to refine a structure at 3.6 Angstrom resolution. The asu consists of 8 copies of hetero-dimers (of roughly 40 KDa sunbunits each). The structure of one of the subunits has already been solved at about 2 Angstrom, whereas for the other no homologous model is available. After automatic + manual building, I have now a model with Rfree = 28 / R = 23, with some protomers better built than others. I have used this pdb model as input for DEN refinement, adding the known higher-resolution structure as a (partial) reference model, and ncs restraints previously found (and run a DEN parameters optimisation). The final DEN Rfee got significantly worse. I would appreciate any advise for a better DEN strategy to be adopted in this case, if possible. In particular I was wondering whether it can be worth building a model for the missing subunit (or part of it) based on structural similarity of the current unrefined 3D structure. I thank you in advance for the suggestions. With kind regards, Marina ----- Marina Mapelli, PhD Department of Experimental Oncology European Institute of Oncology Via Adamello 16, 20139 Milan, Italy tel: +39-02-94375018 email: marina.mapelli(a)ieo.eu web: http://www.ifom-ieo-campus.it/research/mapelli.php -----

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overlapping electron density maps
by 李翔 25 Aug '14

25 Aug '14

Hi everyone, I am working on a series of crystals with overall same framework structure plus a different extra part which attaches to the framework. I want to compare the electron density maps of the crystals by overlapping the frameworks and see how the extra parts differ from each other. Is there a way I can do it? Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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table_one
by Andreas Förster 24 Aug '14

24 Aug '14

Dear all, I encounter the following error when running phenix.table_one from the command line (RHEL 6.3 64-bit, phenix-dev-1769): andreas@csbstereo in blah: phenix.table_one Traceback (most recent call last): File "/csb/soft/Linux64/share/phenix-dev-1769/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/table_one.py", line 6, in <module> phenix.automation.table_one.run(sys.argv[1:], auto_extract_labels=True, AttributeError: 'module' object has no attribute 'run' Aunt Google insists that this is "a circular import issue". What do the developers say? Thanks. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

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Low resolution refinement
by Appu kumar 23 Aug '14

23 Aug '14

Hello All, I have a data from a crystal which we can process to 4.5A, and we are able to get a good molecular replacement model and it is a tetramer in ASU. I tried refining structure with phenix.refine but Rfree stuck at 0.41. I read a paper published by David Baker and phenix developer in 2013 about the low resolution refinement using a combination of rosseta and phenix. I would appreciate if i get a help on the refinement in rosseta along with phenix. This paper convince me that its worth trying the rosseta and phenix together for low resolution structure refinement. Thank you Appu

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Re: [phenixbb] Phenix Webserver Down?
by Chen Zhao 22 Aug '14

22 Aug '14

Thank you all for the info. It is been like this for me for a week, and it might just be some local issues. On Fri, Aug 22, 2014 at 4:20 PM, Paul Adams <pdadams(a)lbl.gov> wrote: > > Appears to be okay from the Bay Area. > > On Aug 22, 2014, at 1:00 PM, Chen Zhao <c.zhao(a)YALE.EDU> wrote: > > > Dear all, > > > > I am sorry to bother you, but I have problems connecting to > www.phenix-online.org. Does anybody have similar problem? > > > > Thank you, > > Chen > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > -- > Paul Adams > Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley > Lab > Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley > Lab > Adjunct Professor, Department of Bioengineering, U.C. Berkeley > Vice President for Technology, the Joint BioEnergy Institute > Laboratory Research Manager, ENIGMA Science Focus Area > > Building 64, Room 248 > Building 80, Room 247 > Building 978, Room 4126 > 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 > ] > -- > > > > > > > > > > > > >

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Phenix Webserver Down?
by Chen Zhao 22 Aug '14

22 Aug '14

Dear all, I am sorry to bother you, but I have problems connecting to www.phenix-online.org. Does anybody have similar problem? Thank you, Chen

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mr_rosetta
by Felipe Trajtenberg 20 Aug '14

20 Aug '14

Dear all I am trying to perform MR of a multidomain protein using phenix.mr_rosetta and building each domain sequentially. The first search works perfect and I have a potential solution. In the second search I am having some troubles in setting up the process. When I fixed the best first model and look for a second domain I found that rosetta only rebuilds the chain A, which was the one that already was fixed and chain B disappears. how can I fix one domain and build the second without loosing any information thanks in advance Felipe

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Stereo Microscope
by jens j birktoft 20 Aug '14

20 Aug '14

Hi: I would be grateful for suggestion regarding stereo microscopes suitable for protein/dna crystal viewing and manipulation. We would need a system that fulfull all of the criteria: 1) Two polarizers one for below the sample holder and one above 2) A fully rotatable stage 3) A camera option, either one that comes included with the unit (the best) or one with a universal camera mount Thanks Jens +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Director of Crystallography Structural DNA Nanotechnology New York University e-mail: jens.knold(a)gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

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Composite Omit Map with Parallel Processing
by Whitley, Matthew J 19 Aug '14

19 Aug '14

Hello all, I am trying to calculate a simulated annealing composite omit map via parallel processing in Phenix 1.9-1692. Our computer cluster uses a PBS que, and jobs are submitted using the 'qsub' command. In the 'Processes' tab under Phenix Preferences, the queueing system is set to PBS, and the queue submit command is set to qsub + additional flags (walltime, etc). All the usual boxes are checked to indicate to Phenix that jobs should be run in parallel when possible. However, when I actually run the composite omit map calculation, the specified qsub flags do not get carried over into the calculation parameters. If I click on Settings-->View all settings in the Composite Omit map calculation window, the qsub_command parameter under 'parallel' is set to None. Because my desired walltime is not being carried over with the qsub command when the calculation starts, the calculation for each individual box is aborting prematurely when it reaches the default process time limit set by our cluster administrator. In the composite omit map calculation in previous versions of Phenix, when clicking "Run" you used to be able to then click "edit parameters and run" in order to check all settings one last time before starting the job. This option does not seem to be available in Phenix 1.9-1692, and thus I can't verify and/or edit the qsub command directly before firing off the job. Any ideas on how to overcome this? Am I missing something? Thanks, Matthew

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