- phenixbb - phenix-online.org

phenix rosetta refine
by Andreas Förster 26 Nov '14

26 Nov '14

Dear all, I'm trying to get phenix.rosetta_refine to run. I think it's all set up properly, with Rosetta 3.5 and Phenix 1810 on RHEL 6.3 64bit. However phenix.rosetta_refine model.pdb data.mtz nproc=48 protocol=full > log& fails with the following error in log: End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it. To me it seems things are defined correctly: andreas@csbstereo in phenix: echo $ROSETTA_BIN /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin andreas@csbstereo in phenix: ls $ROSETTA_BIN | grep scripts rosetta_scripts.linuxgccrelease@ rosetta_scripts.default.linuxgccrelease@ andreas@csbstereo in phenix: ll $ROSETTA_BIN/rosetta_scripts.linuxgccrelease lrwxrwxrwx 1 csbadmin csb 93 Oct 9 2013 /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -> ../build/src/release/linux/2.6/64/x86/gcc/4.4/default/rosetta_scripts.default.linuxgccrelease Any idea of what's wrong would be greatly appreciated. Andreas -- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology Imperial College London

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Alternative conformation of ligand with near zero occupancy
by Singh, Bishal 26 Nov '14

26 Nov '14

Hello everybody, I thank you for clarifying my previous doubts. Your suggestions matter a lot to me. Here I have another doubt. I have structure of a protein in complex with triglycan (fucose-galactose-galactose). The terminal galactose of this triglycan possesses two conformations with occupancies 0.4 and 0.6. In order to satisfy the geometric parameters of this triglycan, I derived the alternative conformation of fucose and the central galactose as well. Then I performed occupancy refinement. The occupancy of alternative central galactose is 0.06 and that of alternative fucose is 0.00. Now the question is, should I delete this fucose of zero occupancy or keep it to maintain the geometric parameters of triglycan? I am looking forward for your opinion. If you like I can provide a snapshot of ligand with electron density. With regards, Bishal Singh PhD student DKFZ, University of Heidelberg, Germany

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input for specifying labin in phenix.find_ncs
by Arka Chakraborty 26 Nov '14

26 Nov '14

Dear Phenix BBers, I have a seemingly trivial problem in specifying column labels in phenix.find_ncs. Following the manual, on entering labels as : phenix.find_ncs xx.pdb yy.mtz params.ncs.labin = "labin FP=F PHIB=PHI FOM=FOM" , phenix returns the error : 'Sorry, cannot interpret the keyword: params.ncs.labin=labin FP=F PHIB=PHI FOM=FOM'. Any clues on what mistake I might be making will be greatly appreciated. Thanks a lot, Regards, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

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Different space group of coordinate and structure factors
by Singh, Bishal 25 Nov '14

25 Nov '14

Hello everybody, For a data-set, the space group after data-processing was P4222. When I performed molecular replacement through PHASER in phenix keeping the search option 'All possible in same point group", the space group changed to P41212. Now the question is that shall I process the data again in this new space group or should I move on for refinement? Please suggest me your opinion. With regards, Bishal Singh PhD Student DKFZ, University of Heidelberg, Germany

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explicit solvent in low resolution refinement
by Guenter Fritz 25 Nov '14

25 Nov '14

Dear all, we have determined the structure of a protein complex at 3.5 A resolution as well as the structures of three subunits of this complex independently at resolutions better than 2 A. I had used the models of the subunits as reference models in refinement, perfect. Now I was wondering whether one could use explicit solvent positions (e.g. inner shell water molecules) from the high resolution structures in the low resolution refinement. This should be superior to a simple bulk solvent model. I placed the inner shell water molecules from the high res structures into the low res model and added harmonic restraints to the water positions in low res refinement. I see a decrease of about 0.5% in Rwork and Rfree versus the model without water molecules. However, adding harmonic restraints excludes the option to use the reference models in refinement. Is it possible to use protein and water atoms from the reference models to generate restraints for the low resolution refinement? Thank you, Guenter

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ready set and H/D addition on waters
by Maxime Cuypers 24 Nov '14

24 Nov '14

hello, after not using phenix for a while, i just realised the new versions do not include the option in ready_set gui to add H or D atoms to waters in the pdb models (and only to the waters without altering the rest of the model would be nice). of course it can be done on the command line but why has it been removed? it is a very neutron crystallographer friendly option don t you think? cheerios, -- Dr. Maxime Cuypers

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Rwork > Rfree
by Singh, Bishal 21 Nov '14

21 Nov '14

Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany

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MRage against local "select" PDB database on commandline
by Kaushik Hatti 21 Nov '14

21 Nov '14

Hi, I am new to Phenix. Sorry if my question is naive. For a given mtz file, I want to pick templates from a local PDB database (its actually iTasser template library) and perform Molecular Replacement using MRage. I have already installed Blast, downloaded iTasser PDB library (http://zhanglab.ccmb.med.umich.edu/library/PDB.tar.bz2) and extracted sequences from both the downloaded PDB template library set and target protein for which mtz is available. How should I go about building pipeline to perform MR using templates from locally downloaded select PDB database? Are there any more parameters available for parameter name: services under scop: search other than "local" and "ncbi"? Thanks in advance, Kaushik -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

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Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 20 Nov '14

20 Nov '14

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2015 issue is 17 December 2014 (with some leeway if you are still working on the text, especially as it can be polished over the break). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Re: [phenixbb] Rwork > Rfree
by Ed Pozharski 20 Nov '14

20 Nov '14

Generate a different test set and repeat refinement. Do it twenty times. If R turns out to be systematically higher than Rfree even in few resolution shells, you have an interesting case worth looking at. If not, it's just noise. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: "Singh, Bishal" <b.singh(a)dkfz-heidelberg.de> </div><div>Date:11/20/2014 9:52 AM (GMT-05:00) </div><div>To: phenixbb(a)phenix-online.org </div><div>Subject: [phenixbb] Rwork > Rfree </div><div> </div>Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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