From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Apr 09 2010 - 04:42:49 CDT

2010/4/9 Knut Jørgen Bjuland <knutjorgen_at_gmail.com>:
> Is it possible to change the the default pH when viewing a protein. I would
> like to see the charge of the protein for pH above 7 ans set it to pH 8.5 as

VMD is a _viewer_ and doesn't know a thing about pH, chemistry
or anything like this. it will show what you feed it. i assume you want
to see the different protonation states of sidechains. in that case you
first have to run a software that computes them, outputs the corresponding
coordinates and then view it.

> an example. Is it also possible to see the amino acid name as is possible to
> do in javamol

i don't know javamol, so i can only guess. in principle, yes, but you
would have to write a script that would identify one atom per residue,
e.g. the alpha-C and then add a label with the corresponding format.
for details please see the user's guide on how to use the atomselect
and the label command and how to write custom Tcl scripts.

cheers,
    axel.

>
> Best regards
> Knut j
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.