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

Francesco Pietra chiendarret at gmail.com
Fri May 12 12:02:53 PDT 2017


Hi Elaine:
That fantastic 'sel sel z<5'!

Thanks a lot

francesco

On Fri, May 12, 2017 at 7:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> -----
> 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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