VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Sat Jun 30 2012 - 09:29:50 CDT

Thanks, but is there no easy way to do this with vmd's naming such as:
label add Bonds 1/(residue 101 and name ca) 1/(residue 125 and name ca)
?
This would be much easier than displaying the atom, then selecting it using
the mouse and reading off its index every time.
Thanks,
Eddie

On Wed, Jun 13, 2012 at 5:47 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Jun 13, 2012 at 5:44 PM, Prof. Eddie <eackad_at_siue.edu> wrote:
> > Hi all,
> > I've tried labeling with the mouse and using different graphical
> > representations of the residues of interest so I can more easily create a
> > bond in the openGL window. It seems tedious. Are there commands to do
> this
> > without clicks if one knows the residues or atom numbers? Something like
> > set label bond residue 150 to residue 7
>
> a) it always helps to read the documentation, e.g. this:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node132.html
>
> b) most (standard) VMD GUI actions have a script equivalent
> you can monitor and even log them to a file. of course this is
> also documented.
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node23.html
>
> if you have not yet noticed, VMD will be more useful, the more you
> know more about it. there is *much* more to it, than what the
> GUI directly exposes. A lot of stuff in the Extensions menu for
> example has been written in Tk/Tcl script based on the script
> functionality of VMD.
>
> axel.
>
> >
> > Thanks!
> > Eddie
> >
> > --
> > _________________________________________________________
> > Edward Ackad, Ph.D
> > Assistant Professor of Physics
> > Computational Nanophotonics
> > Southern Illinois University Edwardsville
> > (618) 650-2390
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> 

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390