From: Axel Kohlmeyer (
Date: Fri Apr 09 2010 - 04:42:49 CDT

2010/4/9 Knut Jørgen Bjuland <>:
> 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.


> Best regards
> Knut j

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.