- Chimera-users - RBVI Mailing Lists

centroid trace problems
by Francesco Pietra 01 Aug '11

01 Aug '11

hello: "centroid" works fine to me in getting the trace of a moving molecule in and out of a protein, using command define centroid radius 0.2 color red :residuename when the residue is unique. In fact, the method has produced extraordinarily illustrative (I am using the words of the referee) in a paper that will appear shortly on Chemistry & Biodiversity. Now I have three diatomic molecules, only one of which is made moving around. In this case define centroid radius 0.2 color red :residuename:residuenumber for the moving residue does not work. What happens is that "red balls" for the specified residue are being accumulated at the place of origin of the residue, while the residue is leaving the protein as a short bar, not a ball. Could that be fixed in the above command? thanks francesco pietra

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hide a peptide in Chimera
by C.J. 29 Jul '11

29 Jul '11

Hi,all, I have a pdb file containing several peptides. And I want to hide some of them when visualizing the file in Chimera. Anyone would like to help me to that? I'm appreciated of any suggestions. -- Regards! C.J.

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Hbond in CLI + cacheDA
by Maciek Wójcikowski 28 Jul '11

28 Jul '11

Hello everyone, I'm trying to compute hbonds for quite large molecular database, so i do it in CLI. I've added cacheDA parameter which speeds up whole process at first by 10 times, although after time cache is getting bigger and bigger operations slows down as one can expect, because Chimera is caching every compound. Is there a way to limit the size of a cache, or even better to tell chimera to cache only protein donors and acceptors? ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek(a)wojcikowski.pl

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Chimera 1.5.3, nvidia quadro 4000 and stereo
by Veli-Pekka Kestilä 27 Jul '11

27 Jul '11

Hello, I found following problem when trying to use Chimera 1.5.3 with stereo in Nvidia Quadro 4000. When starting the chimera in windows I will get error: Error Initializing OpenGL: Couldn't configure togl widget When stating in OpenGL debug mode it starts without any problem. Nvidia driver is 275.65 and everything works in linux without problem. In Manage 3D settings I have put on Stereo Enable. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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gtx-470 GeForce cards
by Francesco Pietra 26 Jul '11

26 Jul '11

With GeForce2 MX200 / Debian GNU-Linux i386 wheezy I have no problems in running movie with "define centroid". In contrast, with GeForce gtx-470 (two such cards and PhenomII 1075T (six cores)/ Debian amd64 wheezy, on running movie to get the trace of the centroid, the X server hangs and the keyboard is no more sensed. I have to restart the computer from a ssh-linked desktop. In both cases chimera 1.5.3. Chimera was started as the only application, just after booting the OS (I am saying that because, to run molecular dynamics, I have first to command # nvidia-smi -L # nvidia-smi -pm 1 Any experience to this regard? thanks francesco pietra

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castp .poc file is not opened in restored session (plain text version)
by Boaz Shaanan 26 Jul '11

26 Jul '11

Hi, I save a session in which I used castp .poc file (very nice indeed!). However, after saving the session, the restored session does not open the .poc file. Is that how it's supposed to be? Cheers, Boaz P.S. sent again in plain text format since it seems the previous html version has been mangled up 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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Query regarding Ksdssp assignment
by Arun Prasad Pandurangan 25 Jul '11

25 Jul '11

Dear Users and Developers, I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera? Looking forward for the advices. Thank you. with best regards, Arun Prasad

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Display of bond between CA's
by Greg Friedland 25 Jul '11

25 Jul '11

Hi, I'm trying to prepare an image from a structure in which I'd like to hide the backbone atoms except the CAs. When I do this for two neighboring residues however a long bond is drawn between the CAs. How can I hide this without hiding the CAs? Thanks, Greg

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creating multimeric units
by ALEXANDER MUCHUGIA 25 Jul '11

25 Jul '11

Hi, My name is Alexander Muchugia, I am a Bioinformatics student at Rhodes University, South Africa and I am working on modelling HIV protease. It is a dimer but Its modelled as a monomer. I was trying to look for software than can convert it as a dimer. I am enquiring if it is possible to use chimera to do it and how can I do it. Regards. Alexander.

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Chimera for Mac OSX Lion
by Victoria James 22 Jul '11

22 Jul '11

Hi there! I was just wondering if you know if the latest build of Chimera will run on Mac OSX Lion? If not, will you be releasing another build soon that will be able to? Many thanks and kind regards Victoria

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