February 2013 - Chimera-users - RBVI Mailing Lists

Blast protein
by Bobo Dang 05 Feb '13

05 Feb '13

Hi guys, I was trying to build homology model using chimera. The uniprot ID of the molecule I want to build is Q9X2V8, when I was trying to blast to find the homologs which have structures. It returns "no BLAST matches found". Does this mean there is no Q9X2V8 homolog from PDB? how does Chimera judge one molecule could match (could be the homolog)? thanks bobo

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pseudo bond reader in command line
by M. Elizabeth Stroupe 04 Feb '13

04 Feb '13

Hi, I am trying to make a figure with pseudo bonds - the figure is fairly complicated and it will be a frame in a movie of related shots, so I need to call the pseudo bonds in from the command line. How do I read in a text file that defines the pseudo bonds (as if from the pseudo bond reader) and then alter their attributes (to make them into dotted rather solid lines)? Thanks much, Beth

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Add hydrogens to DNA
by sette＠uniroma2.it 02 Feb '13

02 Feb '13

Hi, I used the addH to add hydrogens to a DNA pdb file generated with 3DNA but most of the atoms are not protonated. Is addH used for DNA or just for proteins? Thanks, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Re: [Chimera-users] Problem with Chimera 1.7 on Linux OS
by Greg Couch 01 Feb '13

01 Feb '13

Those errors are coming from Chimera asking the graphics driver about multisampled visuals. You might be able to avoid the problem by starting up chimera with the --debug-opengl flag and turning off multisampling. But the fact that you are getting an error means that you need to update the graphics driver on your Linux production computer. For Linux computers, we recommend installing the proprietary NVIDIA or AMD graphics driver depending on which brand of graphics hardware you have. If you have Intel graphics, the only easy way to get updates is to update to a newer version of Linux. If you are running Chimera inside a virtual machine, then updating the graphics driver means updating the virtual machine software, but chimera would perform better without that intervening layer. Also note that on some newer versions of Linux, eg., Ubuntu 12.10, the default setup interferes with OpenGL applications, in particular, opening the SideView tool causes Chimera to crash. The workaround is to switch to a non-compositing window manager like xfce. HTH, Greg On Fri, 1 Feb 2013, Stephen P. Molnar wrote: > I have downloaded, and installed, the 64 bit linux version 1.7, in 64 bit > Debian Testing running in Oracle VirtualBox v4.2.6r82870 before loading it > onto my Linux production computer. The installer ran smoothly without > generating any warnings or errors. > > > > However, when I run the executable I get the following messages: > > > > computation@debian:~/Apps/chimera/bin$ ./chimera > > OpenGL Warning: glXChooseVisual: bad attrib=0x186a0, ignoring > > OpenGL Warning: glXChooseVisual: bad attrib=0x186a1, ignoring > > OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your > SPU > > > > I have the win version open in MS Win 7 on the same computer as I compose > this message. > > > > Stephen P. Molnar, Ph.D. Life is a fuzzy > set > > Foundation for Chemistry Stochastic and > multivariate > > www.FoundationForChemistry.com > > (614)312-7528 (c) > > Skype: smolnar1 > > > > > _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Problem with Chimera 1.7 on Linux OS
by Stephen P. Molnar 01 Feb '13

01 Feb '13

I have downloaded, and installed, the 64 bit linux version 1.7, in 64 bit Debian Testing running in Oracle VirtualBox v4.2.6r82870 before loading it onto my Linux production computer. The installer ran smoothly without generating any warnings or errors. However, when I run the executable I get the following messages: computation@debian:~/Apps/chimera/bin$ ./chimera OpenGL Warning: glXChooseVisual: bad attrib=0x186a0, ignoring OpenGL Warning: glXChooseVisual: bad attrib=0x186a1, ignoring OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU I have the win version open in MS Win 7 on the same computer as I compose this message. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1

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Chimera-users February 2013