- phenixbb - phenix-online.org

pseudotranslation and twinning problem
by Rajeshwer Sankhala 03 Dec '12

03 Dec '12

I am new to crystallography. I have collected data for 26 kDa protein with a maximum resolution of 2.25A in I 41 space group. I have a poor model for molecular replacement (~15-20% identical). When i did xtriage run, it suggested -h,k,-l twinning law and indicated about pseudo-translation. Now when i am running Phaser for molecular replacement i am getting very low LLG (less than 100) and TFZ score (5-6). Can anyone suggest which parameters or setting i should use to improve my LLG score and get a best model for refinement. Thanks Raj

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dev-1227: problem reading in tls parameters from refmac or tlsmd
by Boaz Shaanan 02 Dec '12

02 Dec '12

Hi, In the TLS pulldown I tried to upload tls parameters from either refmac (.tls) or tlsmd (.tlsin) through the 'load' button, according to the suggestion in this section, but it complains about wrong format of the file. Am I doing something wrong? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Specify particular columns from data files on the command line
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all (again)- I'm trying to run DEN refinement in Phenix from the command line. How do I specify certain columns from multiple data files (in my case, 2 MTZ files) to be used? For example, the Rfree flags from one and the hkl data from the other. Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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DEN refinement
by Morten Groftehauge 30 Nov '12

30 Nov '12

Hi guys, Two quick questions about DEN refinement: 1) If gamma refines to 0 does that mean that I should run DEN refinement again with the output model? Or should I do a refinement and then another DEN? Since gamma = 0 the refinement should be allowed a possibility of moving the structure further towards the reference restraints in my mind. 2) If gamma refines to 1 it means that my reference model is inappropriate, right? Not really much of a question, I know. And I know that DEN refinement is in beta but it would be nice if you outputted the optimal gamma and weight for the refinement to the GUI. Actually it would be nice if the did that for geometry weights and xray weights too when one optimizes them. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Error starting Phenix on Linux
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all- After installing the latest version and release of Phenix (1.8.1-1168) onto our Linux workstation and setting the environment for bash, I get the following error upon trying to launch Phenix from the command line: ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory I've never seen this before (previous versions of Phenix have run fine on this machine) and don't know what this file is exactly and where it should be located. Anyone come across this and know if there is a fix (or if I'm just doing something stupid!). Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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Call for submissions for the Computational Crystallography Newsletter (CCN) January 2013
by Nigel Moriarty 30 Nov '12

30 Nov '12

Folks Calling for articles and short communications of interest to structural biologists. The deadline for publication in the January 2013 issue is 31 December, 2012 but if you can send me drafts before the 15th of December we can get started on generating proofs. 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 the template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty, PhD 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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choosing Rfree set with NCS and twinning
by vincent Chaptal 30 Nov '12

30 Nov '12

Dear phenixbb, I am using the "reflection file editor" in phenix 1.8.1-1168 to generate my test set (with the GUI). I have NCS so I ticked the box "assign test set in thin resolution shells". I also have twinning, and want to have my Rfree not biased by twin related reflections. I guess the option "use lattice symmetry to generate test set" is the one I should use for this purpose? I couldn't find much information online about this option. No log file has been generated so I can't check what happened. I am supposing xtriage is ran in the background and if a twin law is found, then used to generate the test set. My output from xtriage is: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -k,-h,-l |PM| 0.249| 0.272| 0.246| 0.200| ----------------------------------------------------------------- And indeed if I check in mtzdmp the output mtz, reflections in the test set are related by (-k, -h, -l); disclaimer: I only checked in the plane (h,k,0). I would like to be sure my Rfree is generated correctly. Alternatively, what would happen when multiple twin laws are available? Is the most probale used? Is it possible to specify the editor which law to use? Thank you for your help. Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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DNA double helix with many molprobity bad clashes
by Benda, Christian 30 Nov '12

30 Nov '12

Hi, I am refining a protein-DNA complex at around 3 A with a standard b-form dsDNA. R-factors are around 24/20 (kinda low for the resolution). Originally, I placed the DNA using coot and now, after several rounds of refinement in phenix, I get a long list of bad clashes from molprobity validation (in phenix) that covers the whole length of the DNA and almost exclusively lists hydrogens from the ribose moiety (whether or not in contact with protein). My question is, - why is phenix.refine not taking care of these clashes (i.e. optimizes the structure such that they go away)?. Am I giving experimental contribution to high a weight (I have "optimize x-ray/stereochemistry" checked)? - if so, can I (and how) restrain geometry for the DNA a little more but leave the protein alone (and does that make sense)? thanks for any help Christian

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phenix.erraser error
by Russell Chan 29 Nov '12

29 Nov '12

Hi, I'm currently trying to use the new command, phenix.erraser, to refine my RNA structure. I generated a ccp4 map and removed the R-free flags, however it generates an error after its starts its first round of minimization. The command I use is: phenix.erraser <mypdb>.pdb <mymap>.ccp4 The error generated is: ################################### Starting SWA_rebuild_erraser.py... Output pdb will be...precursor_chi_erraser.pdb Create temporary directory /home/Russ/Desktop/erraser_test/precursor_chi_erraser_temp/... fixed_res_final in Rosetta pdb file = [] cutpoint_final in Rosetta pdb file = [1, 2, 3, 4, 12, 15, 19, 20, 21, 25, 30, 37, 38, 49, 54, 58, 68, 69, 72, 79, 83, 84, 105, 108, 109, 122, 124, 125, 130, 133, 134, 137, 140, 143, 146, 158, 160, 161, 168, 170, 176, 179, 187, 189, 201, 204, 205, 216, 217, 228, 237, 239, 241, 245, 246, 268, 269, 273, 279, 283, 292, 293, 302, 305, 309, 311] extra_res_final in Rosetta pdb file = [] Starting whole-structure minimization 1... ******************* ERROR ENDING *************** Command 'phenix.python /home/sbgrid/programs/x86_64-linux/phenix/1.8.1-1168/phenix-1.8.1-1168/phenix/phenix/erraser/full_struct_slice_and_minimize.py -binary_name linuxgccrelease -map /home/<Russ>/Desktop/erraser_test/erraser_map.ccp4 -map_reso 2.0 -new_torsional_potential True -pdb minimize_0.pdb -out_pdb minimize_1.pdb > minimize_1.out 2> minimize_1.err' returned non-zero exit status 1 ******************* ERROR ENDING *************** Any help would be greatly appreciated! Thanks, Russell

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Re: [phenixbb] [COOT] CCP4 - Coot in Applications
by Nathaniel Echols 28 Nov '12

28 Nov '12

---------- Forwarded message ---------- From: Paul Emsley <pemsley(a)mrc-lmb.cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: Date: Wed, 28 Nov 2012 17:08:50 +0000 Subject: Re: [phenixbb] [COOT] CCP4 - Coot in Applications On 28/11/12 15:03, Antony Oliver wrote: > > Ok - annoying thing…. > > 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from the command line (terminal window) works IF you don't have X11 open already. > 2) if you DO have X11 open, coot pretty much always crashes with the aforementioned "invalid window errors". It is not clear to me if you are, or are not using Bill Scott's binary... (it's the one I recommend for Macintosh). Paul.

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