[Chimera-users] Alias commands for volume pieces

Benjamin Looker bgl44 at cornell.edu
Wed Oct 17 07:31:49 PDT 2018


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?

Benjamin G. Looker
Graduate Student
Lancaster Group
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