Angel,
Thank you for your suggestions. I will look into them and see if it works
for me.
But, ideally I would like a script that can be used to mutate any given
residue on-the-fly in response to a command such as:
> mutate LYS63 ALA
Amjad
On Thu, Aug 8, 2013 at 1:36 PM, Angel Herráez <angel.herr...@uah.es> wrote:
> **
> 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.
>
>
>
>
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