- Chimera-users - RBVI Mailing Lists

MatchMaker
by sdimicco 01 Mar '16

01 Mar '16

Dear Developer, I am using MatchMaker to compare some peptides. I would like to know if the RMSD value is referenced to the backbone atoms or to whole atom structure. Thank you in advamce. All the best.

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Screen shots from coot
by John Rose 01 Mar '16

01 Mar '16

Hi, I colleague of mine just showed me that pyMOL can display great looking ED images from COOT which were saved in RASMOL format. Is there a way for CHIMERA to do this. John Rose John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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multiple mutations
by Andrew N 29 Feb '16

29 Feb '16

Hello: How can mark (change color) for ~ 100 mutations at once? Is it possible to write a "code" for that? I would like to have random (different) colors for every mutation. It the case, if mutation lay down very close and same color would make it difficult to tell them apart. Another question: How to add a label like "V75" (Amino acid and position, not "V75.A") with all with black color (not the same color that marks mutation on 3D structure)? Thank you. Sincerely, Andrew

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Mutagenesis
by Andrew N 29 Feb '16

29 Feb '16

Is it possible to change a single amino acid to see 3D structure changes? Thank you. Sincerely, Andrew

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Temperature during chimera minimization (pdb)
by Vasantha Kumar 29 Feb '16

29 Feb '16

Dear Chimera user I have calculated the structures of a peptide at 273K (0 °C), then I have extracted low energy structures and minimization them in chimera. I am not sure chimera performed minimization at 273K or 298K. Could any one suggest me at what temperature chimera performs minimization (with explicit solvent), is there is a way to set different temperature. thank you so much in advance... Vince

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Could chimera draw shapes faster?
by Ferdinando Randisi 26 Feb '16

26 Feb '16

Hi! I'm one of the developers of oxDNA ( https://dna.physics.ox.ac.uk/index.php/Main_Page) a code aimed at simulation of large DNA structures for biology and nanotechnology. We often use chimera because, frankly, it makes gorgeous pictures. Since we simulate DNA as made by rigid nucleotides instead of atoms, we hijack it to make it plot various shapes instead of using atoms directly, but it takes forever to get it to load a configuration like the one attached. Could you guys do something to make it faster/give as some advice on how to make it plot these things faster? We currently use the input files attached. (chimera.txt should be renamed chimera.com so that it can be understood by chimera). Best, Ferdinando -- Ferdinando Randisi

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VR support
by Gökhan Tolun 25 Feb '16

25 Feb '16

Hi, Now that the pre-orders are being placed for VR headsets, are you planning to support the headsets like Oculus Rift and HTC-Vive for 3D stereo Opening rendering? Looks like nVidia is making this easier for developers: https://devblogs.nvidia.com/parallelforall/vr-sli-accelerating-opengl-virtu… Thanks. Gökhan

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minimal graphic card
by Fabian Technion 25 Feb '16

25 Feb '16

Hi, I would like to know your reccomendation for a minimal graphic card standard that will work nicely with chimera. It is for 20 PC for a teaching room. Thanks a lot in advance, Fabian Dr. Fabian Glaser Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa 32000, ISRAEL fglaser at technion dot ac dot il Tel: +972 4 8293701 http://bku.technion.ac.il

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Segment according to fitted model
by David Haselbach 25 Feb '16

25 Feb '16

Hi, I do have a cryo EM map of a large complex and I fitted/modeled the individual protein components. Now I would like to segment my map according to those fitted models. Is there a possibility of doing that automatically? Cheers David

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Obtain list of residues in CASTp pocket
by Felipe Vasquez 25 Feb '16

25 Feb '16

Hi, I recently could detect those residues composing certain pocket of my protein, which appeared colored in green at the complete 'sequence' window. However, I wonder if it is possible to obtain these residues as a list (thr59, Val115, etc) useful as a txt or other similar format. Is there some way to achieve this goal? It could be possible for Surfnet also? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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