- Chimera-users - RBVI Mailing Lists

Kaspersky warning
by snoze pa 17 Feb '11

17 Feb '11

While working with chimera my anti virus dtected following virus. Is it a virus or something else. http://imageshack.us/photo/my-images/651/chimeracopy.png/

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Disulfide Bond Question
by Wesley Chen 16 Feb '11

16 Feb '11

Hi, I can make the disulfide bonds show up between two cysteine resides, but I would like to draw the bond between the two alpha carbons. Right now, I can only draw the disulfide bond itself (which just shows a bar that's parallel to both cysteines) or the whole ball/stick model where all the atoms in the residues show up. I'm just trying to draw a simple bond structure between two cysteines (which is already provided in the pdb file). Thanks, Wesley

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Question
by Larry Simpson 16 Feb '11

16 Feb '11

Is there a program to convert Zeiss "zvi" files which are obtained using a Zeiss fluorescence microscope to "MRC" files (Eman files - cryoelectronmicrosopy single particle reconstructions)? I would like to be able to visualize these 3D files using Chimera. Thanks. Larry

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Labels of Metal atoms
by Michael Day 15 Feb '11

15 Feb '11

How do I make the default label for metal atoms be upper and lower case? For instance in an iron compound, if I issue label ~H from the command line the result will be FE1 where I prefer Fe1, etc., etc. This is true for all two letter atom names. Thanks Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------>>>

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choose a specific rotamer
by Elisabeth Ortega 15 Feb '11

15 Feb '11

Hi all, I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h-bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it? Thanks in advance. Elisabeth Universitat Autònoma de Barcelona (Spain)

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Image size reduction
by compchem compchems 15 Feb '11

15 Feb '11

Hello. Dear Chimera users, Is it possible to save part of session screen, not whole picture? I just need in high-resolution illustration. With my best wishes, Dmitry Yegorov.

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My anti-virus software detected a trojan in chimera
by Morais, Marc C. 15 Feb '11

15 Feb '11

Hi, I recently installed chimera 1.5.2 on my laptop (runs windows 7). It installed fine, but when my anti-virus software (Kaspersky) ran a scheduled scan, it claims to have found a trojan in the chimera installation. Specifically, it reports: Virus: HEUR:Trojan.Win32.Generic Location: C:\Program Files\Chimera 1.5.2\bin\ffmpeg.exe Is there a chance the program is actually infected, or is this just a false positive? Thanks, Marc

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dome/image seams
by Dougherty, Matthew T 14 Feb '11

14 Feb '11

I am getting image seams on some camera positions, attached. Any suggestions on how to minimize them? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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movie spatial sizes
by Dougherty, Matthew T 14 Feb '11

14 Feb '11

Normally I am generating movies at 640x480 or 1280x960. My graphics display is 2000x1500. I need to generate movies at 4000x4000 & 2000x2000. When I set the window size to 4000x4000 it limits it to the graphics display. How do I generate movies at the larger size? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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How to assign a unique chain ID to a receptor with two chains
by Qin Shao, Mr. 12 Feb '11

12 Feb '11

Hello I am currently using Chimera 1.5 to analysis docking simulation results from HadDock, because one of my receptor has two chains, it cannot be accepted directly. Through a communication to HadDock, I was advised that I should avoid overlapping numbering between the two chains and use a unique chain ID. Could you tell me whether I can do it on Chimera based on Windows platform, how to do it. Thank you very much. Best regards Dr. Qin Shao Montreal Neurological Institute McGill University Montreal, Canada

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