Hi Amjad
I've heard that question several times and I always reply "it cannot be done
in Jmol, you need a modelling software".
This is really tricky. I mean, the result is hardly reliable. But I see your
point.
I haven't seen what PDBViewer does for that.
I would say this is a reasonable way to approach, with all the caveats:
1. Load the protein.
2. Load a single amino acid (the mutated one). For example, from PubChem
or Cactus
3. Remove atoms from the amino acid that will not be part of the protein (i.e.
H from amino and OH from carboxy)
4. Use the "compare" command in Jmol to align the new amino acid to the
old one in the protein. Probably you need to specify the N and C atoms,
maybe the whole backbone, so the new residue will match the orientation of
the old residue.
5. Delete or hide atoms from the old residue
It's a nice exercise -- but not trivial to get done. I might be interested in
working on it with you.
------------------------------------------------------------------------------
Get 100% visibility into Java/.NET code with AppDynamics Lite!
It's a free troubleshooting tool designed for production.
Get down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
