[Chimera-users] Visualizing specific atoms in autodock-vina output

Elaine Meng meng at cgl.ucsf.edu
Fri May 12 10:36:56 PDT 2017

Hi Francesco,
Although each atom in a residue should have a different name, I guess your model #1.1 has more than one residue.  If you hover the mouse over the atom you are interested in, the pop-up information should include both the residue number and the atom name, which you can include in the command to narrow it down, for example:

sel #1.1:2 at N z<5

(atom named N in residue 2 of model 1.1).  Or, if you don’t mind doing it interactively, you could Ctrl-click to select the atom you want and then use “sel” to specify it, for example:

sel sel z<5

Although you might think that wouldn’t work, it does!
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 May 12, 2017, at 10:26 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> I am trying to investigate the protein surrounding a docked (autodock-vina, alpha chimera 1.1 build 40505 linux 64) ligand. I am interested in the environment of specific atoms of the ligand.
> With command
> sel #1.1 at N z<5
> I can investigate the protein at 5A from BOTH nitrogen atoms of model 1.1.
> How to select one of the two existing N atoms in the ligand? Same questions for other ligand atoms (there are many O-atoms)
> Is that possible without elaborating the vina output?
> thanks
> francesco pietra

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