April 2012 - Chimera-users - RBVI Mailing Lists

About volume viewer in chimera 1.6.1
by Yuhong Li 30 Apr '12

30 Apr '12

Dear Chimera developers, Hi! I am a student from Sun Yat-Sen University. I recently began using the Chimera for my study, but I have a problem about how to read the displayed information in volume viewer. Here I attach a picture and inside the picture there are two places I've point out with arrows which represent two different map files in mrc fornat. Now I was wondering if you could spare some time to explain it to me that what do those different numbers mean? Hope to hear from your reply in very soon. Best Wishes, Yuhong Lee

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addaa command
by Mahendra B Thapa 27 Apr '12

27 Apr '12

Dear chimera users, I also added an amino acid residue at the N-terminus of a small protein following the posting: [Chimera-users] Using addaa at the N-terminus?*[ posted date:Fri Sep 30 10:36:31 PDT 2011]* The residue is added at the n-terminus but the added residue is not connected to rest of the protein structure in the graphical display [i.e, a little gap between the added residue and the rest of the protein at N-terminus]. Is this due to wrong command ? Thanks, Mahendra Thapa Graduate student Department of Physics University of Cincinnati, OH

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Per model clipping not working ?
by Damien Larivière 27 Apr '12

27 Apr '12

Dear all, I try to use the Per-Model clipping tool but this error is returned, whatever the PDB file: Model cannot currently be clipped [no valid bounding box] Do I make something wrong? I use Chimera version 1.6.1 (build 35849). My configuration is Windows 7 64bits, ATI Mobility Radeon HD5650. Many thanks for your help! Damien

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loading trajectories with no box line
by Michael F. Bruist 25 Apr '12

25 Apr '12

Is there a way to load trajectories that do not have box lines? I have trajectories from which most solvent and ions have been stripped. They were written with ptraj as amber coordinate files with the "nobox" option. I cannot get these to stay in register for MD movie. I do not have this problem for trajectories for which the box line has not been removed. Mike Bruist Dr. Michael F. Bruist Associate Professor of Biochemistry Department of Chemistry & Biochemistry Griffith Hall 147 University of the Sciences in Philadelphia Philadelphia, PA 19104-4495 Phone (Office & Voice Mail): (215) 596-8530 Department Phone: -8839 Department Fax: -8543 E-mail: m.bruist @usp.edu web page: http://tonga.usp.edu/bruist

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saving transformed map
by Elaine Meng 25 Apr '12

25 Apr '12

On Apr 25, 2012, at 9:04 AM, Ariane Briegel wrote: > Dear Elaine, > I have been using chimera to align several EM maps in respect to each other. > These maps are generated by imod (mrc format). I know I can save the transformed maps in chimera when I use the 'save session' command, but that only allows me to use the transformed maps inside chimera. I would like to save the individual transformed maps- either in mrc or CCP4 format. > I tried to find any info about that in the manual, then checked the old chimera list comments. I found a similar question from the year 2006 (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-July/000864.html), but at that time your conclusion was it is not possible. > Do you know if there is a way to do this now? > Thank you so much for your answer, > Ariane Hi Ariane, The map formats don't include transformation information, so there is no way to save EXACTLY the same data, except transformed. However, you can resample the map onto a new grid, and then save the new map. The values at the new grid points are determined by interpolation, so there will be some (generally minor) data loss. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> The resampling of one map onto the grid of another can be done with command "vop resample" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> For example: vop #1 resample onGrid #0 To save the resampling result to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its "save" option. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Chimera-users Digest, Vol 108, Issue 25
by Boaz Shaanan 24 Apr '12

24 Apr '12

Hi, Elaine is correct in that newly deposited structures (since a year or so?) have to have their TLS information converted to aniso B and have those values in the appropriate place on the ATOM card. However, this was not the case for the older entries. The 1ss8 entry seems to have been refined by refmac5 from the ccp4 package. In this package there is a program called tlsanl which will do the job of converting the TLS infotmation to B-aniso. (a several seconds job) So maybe Steve could use it and thus solve his problem? Cheers, 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 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Tuesday, April 24, 2012 7:19 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 108, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: remote session (Greg Couch) 2. Rendering TLS information in Chimera ? (Steven Ludtke) 3. Incomplete chain contain many dotted lines while displaying (Junfeng Huang) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Apr 2012 12:05:41 -0700 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] remote session Message-ID: <4F95A805.1080609(a)cgl.ucsf.edu> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" The error is that the OpenGL library is looking for a NVidia-specific extention to the remote protocol and failing when it is not there. That is a driver bug -- it shouldn't matter what graphics driver you have on either of the systems. There are two things I'd do to try and fix it: (1) try updating the NVidia driver on the remote computer that is running chimera (not the computer displaying chimera), and (2) try uninstalling the NVidia driver on the remote computer, and reverting to the software implementation of OpenGL (mesa). The first option is preferable if it works, because the proprietary (NVidia/AMD) drivers have been faster and less buggy than the mesa driver for most uses. Good luck, Greg On 04/20/2012 02:25 PM, Hernando J Sosa wrote: > > Hi > > I used to be able to run chimera remotely from a machine with an X- > windows server (the one that comes with Cygwin in this case). But now > I get the following error: > > Xlib: extension "NV-GLX" missing on display "localhost:10.0". > > X Error of failed request: BadRequest (invalid request code or no > such operation) > > Major opcode of failed request: 148 (GLX) > > Minor opcode of failed request: 181 () > > Serial number of failed request: 12779 > > Current serial number in output stream: 12784 > > I t does work fine if run directly from the computer where chimera is > installed. Any idea what the problem could be? > > Thanks > > Server computer: > > Chimera v 1.5 (similar problem with 1.6) > > OS: Linux OpenSuse 11.3 64b > > Client computer: > > OS: Windows 7 64. > > Graphics: ATI Radeon HD 5450 >

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electron density ven diagram
by Terry Lang 24 Apr '12

24 Apr '12

Hey Guys, I am interested in making kind of a ven diagram between two maps for electron density (see attached). What I would like to do is where the density is above a certain threshold for both maps, color the map grey, and where it is above the threshold for map A only, color red, and for map B only, blue. Plan #1 --superimpose maps (have this working) --create a third map (have this working) --do a direct < > = point-by-point comparison between map A and B and reset the values of the third map to be -1 (map A only), 0 (both maps) or 1 (map B only) --color the map using the histograms PROBLEM: The maps are not gridded the same. After some careful thought, I don't think I actually can get them gridded the same for technical reasons. Plan #2 --superimpose maps (have this working) --create copy of map A (coarser map) with map A gridding (have this working) --use interpolation function to interpolate map B (finer map) onto map A gridding --create copy of map A and do a direct < > = point-by-point comparison between map A and interpolated map B and reset the values of the fourth map to be -1 (map A only), 0 (both maps) or 1 (map B only) --color the map using the histograms QUESTION: Is there an easier way to do this with tools that already exist in Chimera? If not, can I get a little bit of info on how the data is stored in the ccp4 style maps (eg start at origin and loop over x, loop over y, loop over z or something else?) Let me know if you need more details or clarification on this rats nest. Thanks! Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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Incomplete chain contain many dotted lines while displaying
by Junfeng Huang 24 Apr '12

24 Apr '12

Hello Everyone， I have a problem while display PDB file. I extract the residues from protein-protein interface by ligplus into a new PDB file, and want to display and analysis it. As the file contain only the residues form interface, they are discontinuous. While display with pymol, it is OK. However, While using Chimera, there are many dotted lines between the residues. I know what the dotted lines are, but I do want to hide all these lines, can somebody please give me some hints? I sent two figures in the attachment. It's the first time I used mail-list, if it doesn't support figures, please check here: Interface display by pymol http://bbs.sysu.edu.cn/attach/Pictures/1335235173.JPG Interface display by Chimera http://bbs.sysu.edu.cn/attach/Pictures/1335235254.JPG Thank you very much!

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Charge data
by Nikolay Igorovich Rodionov 24 Apr '12

24 Apr '12

Hi everyone, I know chimera does not produce PQR files, but I was wondering if it is possible to create a data text file with the atoms' three dimensional coordinates and charges after applying the amber forcefield? Sincerely, Nikolay Rodionov

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Rendering TLS information in Chimera ?
by Steven Ludtke 24 Apr '12

24 Apr '12

Hi. A question about rendering B-factor information: Over the last decade, rather than simple anisotropic B-factors, it has become increasingly common to represent local "motion" using the translation-libration-screw (TLS) model, which provides for anisotropic representation of such motions. Is there a good way to represent this data in Chimera ? Here is an example. If you render the PDB structure 1OEL as atoms, and color the atoms by B-factor, you can immediately observe regions of high variability in the apical domain. This same data was later re-refined using a TLS model as PDB structure 1SS8. When you render this structure in Chimera in the same way, you see high B-factors only for a few specific sidechains. The overall large-scale variability is gone, presumably because the TLS parameters have absorbed it, and the "B-factor" is now only a residual B-factor. However, I can't see any obvious way of rendering the TLS information. Any tips ? ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu) Co-Director CIBR Center (www.bcm.edu/research/cibr) Dept of Biochemistry and Mol. Biol. (www.bcm.edu/biochem) Baylor College of Medicine sludtke(a)bcm.edu stevel(a)alumni.caltech.edu

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Chimera-users April 2012