[Chimera-users] Alias commands for volume pieces

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 17 10:54:50 PDT 2018

Hi Benjamin,
Can you please provide an example file as an attachment so we don’t have to guess what it contains?

If it is indeed 2 surface pieces of a single model, then I believe my previous reply applies, and there isn’t a way to specify the pieces separately in the “volume” command, sorry. Although you can select one of the pieces with the mouse and not the other, and then use “sel” as the command-line specification, the “volume” command still acts on the whole model, or at least it did when I tried it just now on my example electrostatic potential (ESP) file with positive and negative isosurfaces.

However, we’d need one of your files as an example to fully understand your situation.  We have tried other cube files but their contents are not representative of all cases.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 17, 2018, at 7:31 AM, Benjamin Looker <bgl44 at cornell.edu> wrote:
> Hello!
> I have recently received emails from Tom Goddard and Elaine Meng on this subject, but I believe it can be further clarified. 
> The research group I am a part of routinely generates Gaussian cube files  for molecular orbitals using the DFT program ORCA, we then manually use Chimera to change the level and color of the two phases of the resulting wave function, which appear in Chimera as two surface pieces belonging to the same surface. 
> In the volume viewer menu Data, and in the Model Panel, there is no way to see a #0.1 #0.2 model subnumber, and Group/Ungroup returns the error "Cannot group a single molecule."
> Is there a way to refer to volume pieces in the command line? Such that an alias can be written to do this formatting in a more efficient manner? 
> Best, 

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