- Chimera-users - RBVI Mailing Lists

Python code problem
by Mahendra B Thapa 29 May '15

29 May '15

Dear Chimera users, The command I used was chimera --nogui test.py I tried two codes (following previous posts and tutorials in chimera) in 'test.py' as follows (i) import os from chimera import runCommand as rc from chimera import replyobj rc("open " + 'test.pdb') for i in [2011,2420]: rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) *This code gave the result as expected*: Executing test.py... Opening test.pdb... 60 models opened Distance between #0.2:2010.B@CB and #0.1:2011.B@CB: 72.346 Distance between #0.2:2010.B@CB and #0.1:2420.B@CB: 92.979 Executed test.py (ii) import os from chimera import runCommand as rc from chimera import replyobj rc("open " + 'test.pdb') for i in range(2011,2420): rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) *This code gave the result as* ' You selected %d.' % numSelected) MidasError: Exactly two atoms/axes/planes must be selected. You selected 1. Error while processing test.py: MidasError: Exactly two atoms/axes/planes must be selected. You selected 1. File "/opt/UCSF/Chimera64-1.5.3/share/Midas/__init__.py", line 1266, in distance ' You selected %d.' % numSelected) What could be the error this code? Only difference between two codes is: "for * i in [2011,2420]:" & "for i in range(2011,2420):"* That is, I am interested to use range operator in 2nd case instead of two values as in the 1st case. Thank you for help, Mahendra Thapa University of Cincinnati,OH

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Ramachandran plot for a selection
by Elena Lilkova 28 May '15

28 May '15

Dear Chimera community, First I would like to just say that I am new to Chimera. I made a MD simulation of a protein using NAMD. Now I am interested in generating a Ramachandran plot for the whole trajectory, but only for a specific selection of my protein, namely three specific residues. I fail to succeed. Could anyone probably suggest a solution? Elena Lilkova elilkova(a)phys.uni-sofia.bg PhD student, Atomic Physics Department, Faculty of Physics, University of Sofia "St. Kliment Ohridski" 5 James Bourchier Blvd. 1164 Sofia, Bulgaria Elena Lilkova elilkova(a)phys.uni-sofia.bg PhD student, Atomic Physics Department, Faculty of Physics, University of Sofia "St. Kliment Ohridski" 5 James Bourchier Blvd. 1164 Sofia, Bulgaria

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Distances in biological assembly
by Mahendra B Thapa 27 May '15

27 May '15

Dear Chimera users The biological assembly of a virus in pdb format consists of 60 models; each model with 3 chains :A, B and C. I am interested to find atoms within 4 angstroms of the atom, say CA atom of residue 2059 of chain B of model 2. The chimera crashed in graphical interface (it could be due to size of the pdb file.), so I used the following command [ http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-November/002069.html ]: chimera --nogui file_test.cmd > data_rest.log where 'file_test.cmd' consists of open test.pdb findclash #2:2059.B@CA overlap -4 hbond 0 The output file 'data_rest.log' consisted of Opening test.pdb... 60 models opened Opened test.pdb containing 60 models, 677040 atoms, and 89700 residues No contacts No contacts *I want to know whether I have used right chimera command /code. *Any suggestion might help me. Thank you, Mahendra Thapa University of Cincinnati,OH

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scale bar
by Dmitry 27 May '15

27 May '15

Dear developers, How are you? I have a question about scale bar. I am not completely sure that the scale bar I drew is correct. What are the scale settings for drawing the scale bar? By the default the scale bar is in Angstroms isn’t it? In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc) Is there the same possibility in Chimera? Thank you Sincerely, Dmitry

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Starting multiple copies of Chimera on Mac
by Tom Goddard 26 May '15

26 May '15

It is possible to run multiple copies of the same Chimera on a Mac. Here’s how. From a Terminal (/Applications/Utilities/Terminal) type the command open -n -a Chimera The -n option tells the Mac to start another copy of the application. If you prefer to start the second copy by clicking an icon then you can make that icon using /Applications/Automator, choose to make an Application, select Run Shell Script, enter the command open -n -a Chimera as the script to run, then File / Save… to save this application as “Chimera+” or whatever you want to call it. This icon always starts a new copy of Chimera so you can have as many running as you like. Tom

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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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