August 2016 - Chimera-users - RBVI Mailing Lists

Volume and mesh data simultaneously? Coordinate space is different
by Marvin Albert 03 Aug '16

03 Aug '16

Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap). Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh? (this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3 <http://www.filedropper.com/cube_3>) Thanks a lot in advance, Marvin

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precalculated void representation as surface
by Michalska, Karolina M. 03 Aug '16

03 Aug '16

Hi, I have a precalculated cavity represented as a grid in the pdb format, where “atoms” are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface. I appreciate your help, Karolina

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APBS webservers not working
by Ursula Schulze-Gahmen 02 Aug '16

02 Aug '16

I used to run APBS from within Chimera. But recently, the webservers that are called for the APBS calculations are not working. Do I need to go to the APBS website directly or what is the solution? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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chimera 1.11 question
by Dixon, John 01 Aug '16

01 Aug '16

Hi I was wondering if you could help When I install chimera on my main physical PC I can use function left CTRL and mouse to highlight atoms in green in the graphics interface as below. [cid:image003.jpg@01D1E728.1FE9F730] However when I install chimera on a virtual PC, this function does not work. Any ideas on how to get around this issue? thanks John Dixon Application Integration Team Client Platform Services Information Services Division, UCL Tel: 02076799163 Ext: 09163

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