[Chimera-users] question on volume viewer usage

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 4 08:07:58 PST 2011

Hi Bala,
By default, all models track the transformation of the lowest-number model.  However, you can easily apply the transform of one model to another with matrixcopy.  For example, if your structure is model 3 and its potential file is model 5, try command:

matrixcopy 3 5


For your second issue, I don't think you can specify detailed default settings before opening the data.  However, you could use the command "volume" to control the settings.  Once you have figured out the volume command that shows your potential file the way you want it, you could alias it to some short command.  The alias could also be included in a top-level Chimera "Aliases" menu.  For example:

alias ^volfix volume all show style mesh level -2.5 color red level 2.5 color blue

(that should all be one line, the e-mail list software will probably break it up).  Then you can use command "volfix" on the command line, or choose it from the Aliases menu.  For transparent colors, instead of color names you can use R,G,B,A values where A is 1-transparency.

See alias and volume manual pages:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 4, 2011, at 3:28 AM, Bala subramanian wrote:

> Friends,
> I am using chimera version 1.5 (build 31401 downloaded on 2010-09-16). I have three pdb files (of same protein) and for each pdb file, i have an electro static potential file (.dx file). I opened the three pdb files and then the .dx potential files successively through volume viewer. Each time i open the .dx file, the isosurfaces are mapped on to the first pdb file. Why is it so ?. 
> 1) Precisely 1.dx should be mapped on 1.pdb, 2.dx on 2.pdb...etc. How can i do this ?
> 2) Is there any way to have a universal setting of volume display options. Like in isosurface threhold (+2 and -2 in my case), color for +ve and -ve surface, transparency etc. Because presently i am doing these settings individually for each .dx file.
> Thanks,
> Bala

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