[Chimera-users] APBS

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 5 12:04:22 PST 2012

Hello Anjana,
Are you sure you're using Chimera?  As far as I know there is no APBS plugin for Chimera, only for Pymol.

In Chimera,
(A) there are several ways to show distances, including selecting two atoms (Ctrl-click on one atom, Shift-Ctrl-click on the second atom) and using command: distance sel

(B) there is no tool especially for aromatic interactions, but you can use the tool Find Clashes/Contacts or command findclash to  identify contacts between two sets of aromatic residues.  For example, to identify contacts between aromatic amino acids in chain A and aromatic amino acids in chain B, command:

findclash :.a&aromatic test :.b&aromatic overlap -1 hb 0

(You would probably also want to display all atoms so you can see where the contacts are.)

The same thing could be done using the Find Clashes/Contacts graphical interface, in the menu under Tools... Structure Analysis.   GUI documentation:
Command documentation:

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 Jan 4, 2012, at 9:02 PM, Anjana Ramnath wrote:
>       Hello all,
>             My question is simple: im trying to install the APBS plugin but have so far been unsuccessful. I am also trying to show the interactions between aromatic residues on a PDB molecule. how do i do this? im also having trouble with showing the distance between 2 residues. im using Fedora 12 and also WindowsXP. please do let me know. thank you very much!
> sincerely,
> Anjana.

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