May 2015 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] On the seeking of the orthologs
by James Starlight 25 May '15

25 May '15

Elaine, George, thank you very much for the suggestions and ideas!! One question- do you know some DB where is possible to seek for the orthologs (e,g based on HMM) agains *several* target sequences with flexible options like to detect minimal percent of the homology for orthologs which to be found or alternatively to make such search based on some *shared* features between those targets (e.g common structural motifs responsible for ligand binding etc) which might be specified by user initially? George, the idea to focus on particular specie seems interesting- initially I've thought in the same way but to focus on the human OR (because here I'm more comfortable with dynamical range patterns of those receptors based on the in vivo Matsunami data for instance). BTW briefly have a look on those DB I didn't find there engine to seek for the orthologs agains given target. Doest this option really exist within it? All the best, James 2015-05-22 21:10 GMT+02:00 George Tzotzos <gtzotzos(a)me.com>: > I would start from BioMart. I’m also working on OR (albeit insect ones). Try also MGI (Mouse Genome Informatics). Starting from mouse Ors you can scoop orthologs in other mammalian species. > > Cheers > > George > >> On 22 May 2015, at 18:44, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi James, >> Your questions are more about bioinformatics project design rather than Chimera use. >> >> Chimera provides basic BLAST searching of NCBI’s “nr” and “pdb” sequence databases, but these are the same databases generally used by BLAST whether you use it from Chimera or from another program, or stand-alone. Also, Chimera can fetch specific individual sequences from UniProt based on UniProt identifier, but that isn’t searching, it is just getting data you already knew you wanted. >> >> I believe NCBI’s “nr” and UniProtKB are both meant to be comprehensive (cover “all” sequences) but in their own ways, and you would have to go to those resources or their publications to learn the details. There are probably also specialized GPCR and/or olfactory receptor sequence databases. Then there are multiple ways of searching, with individual sequences or with derived patterns such as hidden Markov Models (HMMs). This is a really broad topic and in my opinion, beyond the scope of this forum. You’ve probably done some of this already, but I would recommend reading similar studies in quality journals by authors you respect, to see how they have designed their projects. >> >> Chimera doesn’t have HMM-related tools or evolutionary trace, it just allows conservation analysis on your whole alignment, or subsets of that alignment opened in separate windows. >> >> 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 >> >> On May 22, 2015, at 9:22 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >> >>> Dear Chimera users! >>> >>> I'd like to ask some suggestion regarding my bioinformatician task and >>> possible ways of its realisation using some bioinformatics methods >>> implemented in Chimera. >>> >>> 1)I need to seek for some sequence database (here I don't know >>> absolutely how to do it) of the olfactory receptors and to select 10 >>> sequences of the Ors corresponded to 10 different mammalian species -> >>> according to my idea it should be very different species associated >>> with different ecological niches so its olfactory spectrum should vary >>> dramatically. >>> Here the question: in what DB such search should be better with the >>> inclusion of flexible search criteria's like what I've listened above? >>> >>> 2)After allocating of those 10 sequences I should to find *all* >>> possible orthologs against them-> to find all OR in another species >>> which have conservation degree agains target above chosen threshold . >>> Eventually I'll need to make some analysis regarding overall >>> conservation of the OR within different species and to point out what >>> OR are most important (conservative) in different organisms in >>> accordance to some pre-defined criteria's (i.e ecological niche of the >>> species because it's associated with the odor spectrum). Here the >>> question: would the methods like blast-search be enough for such task >>> or I should to use also methods like evolutional tracing (to find all >>> important residues in different OR which tend to co-evaluate) based on >>> its alignment data? >>> >>> I would be very thankful for any suggestion! >>> >>> James >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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On the seeking of the orthologs
by James Starlight 22 May '15

22 May '15

Dear Chimera users! I'd like to ask some suggestion regarding my bioinformatician task and possible ways of its realisation using some bioinformatics methods implemented in Chimera. 1)I need to seek for some sequence database (here I don't know absolutely how to do it) of the olfactory receptors and to select 10 sequences of the Ors corresponded to 10 different mammalian species -> according to my idea it should be very different species associated with different ecological niches so its olfactory spectrum should vary dramatically. Here the question: in what DB such search should be better with the inclusion of flexible search criteria's like what I've listened above? 2)After allocating of those 10 sequences I should to find *all* possible orthologs against them-> to find all OR in another species which have conservation degree agains target above chosen threshold . Eventually I'll need to make some analysis regarding overall conservation of the OR within different species and to point out what OR are most important (conservative) in different organisms in accordance to some pre-defined criteria's (i.e ecological niche of the species because it's associated with the odor spectrum). Here the question: would the methods like blast-search be enough for such task or I should to use also methods like evolutional tracing (to find all important residues in different OR which tend to co-evaluate) based on its alignment data? I would be very thankful for any suggestion! James

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clustering
by Rafael Rocha 22 May '15

22 May '15

hello, I have a set of ligands that share Some atoms in common. How I can clustering only those atoms? Also, how I can change the variation of RMSD for this cluster analysis in the "ensemble cluster" tool of chimera? Thanks, Rafael.

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chimera improvment suggestion
by Michał Kadlof 21 May '15

21 May '15

I have small improvement suggestion: Is it possible to display directories in Open File dialog with different font than files, for example bold? I'm loosing a lot of time on scrolling my directories tree to find particular file to open. Highlighting of directories would be very handy. -- best Michał

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Re: [Chimera-users] How can I calculate RMSD with chimera script
by Eric Pettersen 19 May '15

19 May '15

Since runCommand() doesn't return any value, you need to call the underlying Python rmsd() function, which isn't hard to do. Somewhere at the top of your script put: from Midas import rmsd and then replace: rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k)) with: val = rmsd("#0:{0}-{1}".format(s,k), "#1:{0}-{1}".format(s,k)) --Eric On May 19, 2015, at 12:45 PM, Michał Kadlof <ramidas(a)gmail.com> wrote: > Yes it work, but then I have to write and run another script to parse output from chimera which cost HDD access time. I was wonder, if it possible to do it in single script without dumping output to separate file. > > -- > Michał > > 2015-05-19 18:53 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: > Hi Michał, > Redirecting output from a program into a file is pretty easy in any Unix/Linux shell. This would redirect Chimera's non-error output into a file named "chimera-output.txt": > > chimera chimera-arguments-you-normally-use > chimera-output.txt > > You can also redirect the error output, but the syntax for that depends on the shell you are using. You should be able to easily Google it if you need to do that. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On May 19, 2015, at 1:16 AM, Michał Kadlof <ramidas(a)gmail.com> wrote: > >> Hello, >> >> I have a need of calculating about 1000 of RMSDs between two particular regions of reference model and testing model. I would like to do this with chimera script. I'm using chimera-1.10.1-Headless Linux 64-bit and have no access to any GUI. >> >> Currently my script looks like this: >> >> import sys, os, re >> from chimera import runCommand as rc >> >> << not important stuff >> >> >> rc("open %s" % (native)) >> for i in models: >> rc("open " + i) >> rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k)) >> rc("close #1") >> rc("close all") >> rc("stop now") >> >> This allow me to see output on the screen, but I don't know how to capture it for further processing. I found somewhere something like this: >> >> from chimera.tkgui import saveReplyLog >> << do something >> >> saveReplyLog('replyLog.txt') >> >> But it seem to work only in versions with GUI. >> >> Please help. >> >> -- >> best whishes >> Michał Kadlof >> >> University of Warsaw >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Load AMBER parm/traj from command line.
by ros 19 May '15

19 May '15

Hello! Is it possible to start up chimera and have it load an AMBER topology and trajectory file? For example, in Linux, you can start VMD with: vmd -parm7 name.prmtop -netcdf traj.nc And will load the topology with the corresponding trajectory frames. In chimera we do that using the 'Get Ensemble info' window in the MD movie tools. Is it possible to do it in a single line? Thank you! Rodrigo.

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How can I calculate RMSD with chimera script
by Michał Kadlof 19 May '15

19 May '15

Hello, I have a need of calculating about 1000 of RMSDs between two particular regions of reference model and testing model. I would like to do this with chimera script. I'm using chimera-1.10.1-Headless Linux 64-bit and have no access to any GUI. Currently my script looks like this: import sys, os, re from chimera import runCommand as rc << not important stuff >> rc("open %s" % (native)) for i in models: rc("open " + i) rc("rmsd #0:{0}-{1} #1:{0}-{1}".format(s,k)) rc("close #1") rc("close all") rc("stop now") This allow me to see output on the screen, but I don't know how to capture it for further processing. I found somewhere something like this: from chimera.tkgui import saveReplyLog << do something >> saveReplyLog('replyLog.txt') But it seem to work only in versions with GUI. Please help. -- best whishes Michał Kadlof University of Warsaw

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depth cue by color for tomogram
by Michael Elbaum 18 May '15

18 May '15

Hello all, I noticed a new sort of 3D color glasses (http://chromatek.com/) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses. I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient. thanks for any help, Michael Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138

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Select multiscale model surface pieces with command lines
by TUBIANA Thibault CNRS 18 May '15

18 May '15

Hi everyone! I Want to script a movie, but to do so, I need to select some surface pieces of a virus multiscale model with command line. I didn't find any way to do that. I try to select them with the mouse (ctrl+click) and then rename the selection with "namesel", it works but when I save the session and reload it, theses selections are cleared.... I can't do that each times I load my session because I have plenty of them and it's to generate the movie on SSH on another computer more powerfull... I can't split them to create a new model (for exemple with coordinates) because I will have to update all my "savepos" position... Did someone know how to do that ? Thank you a lot for your help, Regards, -- Tubiana Thibault PhD Student Institut de Biologie Intégrative de la Cellule CNRS UMR 9198 CEA-Saclay, Bâtiment 532 - Pce 12A 91191 Gif-sur-Yvette 06.79.90.95.85 http://www.tubiana.me

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Problem running Chimera remotely on CentOS7 system
by "Kestilä, Veli-Pekka" 12 May '15

12 May '15

Hi, I have following error when trying to run Chimera remotely on CentOS7 system from OSX this seems to affect also Windows with Xming libGL error: dlopen /usr/lib64/dri/swrast_dri.so failed (/opt/sci/UCSF-Chimera64-1.10.1/lib/libgcc_s.so.1: version `GCC_4.7.0' not found (required by /usr/lib64/dri/swrast_dri.so)) libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1359 Current serial number in output stream: 1359 On windows the error is: ibGL error: dlopen /usr/lib64/dri/swrast_dri.so failed (/opt/sci/UCSF-Chimera64-1.10.1/lib/libgcc_s.so.1: version `GCC_4.7.0' not found (required by /usr/lib64/dri/swrast_dri.so)) libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 145 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1350 Current serial number in output stream: 1350 How I can get this to work? Intended use would be in classroom where we don't have permissions to run or install Chimera. Greetings, Veli-Pekka Kestilä -- Veli-Pekka Kestilä / Huone 4318 / Biokeskus 3 (Viikinkaari 1) / 050-3000014

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