Coot ,Pymol or Mumbo are all software can be used to mutate residues of PDB.
Rotamers can adjust by Coot and you can use Mumbo to do energy
minimisation .As for Pymol ,the powerful fig maker ,is not good choice
to do this .
Maybe Chimera is another choice . But I have not use it before. So I
suggest you to use to Coot or Mumbo.
ta
liu
Juergen Bosch wrote:
In that case you might want to use CNS with model_anneal.inp or
model_minimize.inp, or the equivalents in phenix
Jürgen
On 2 Dec 2008, at 21:29, Hongmin Zhang wrote:
Yes, it is better to have MD or energy minimization. Otherwise, with
only view on the screen, we can't tell if the mutated residue would
disturb ligand binding because of the side chain flexibility.
Best!
Hongmin
On Wed, Dec 3, 2008 at 12:50 PM, Juergen Bosch
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
Pymol
the question is, into how much trouble do you want to get ?
MD simulations ? Energy minimisation ? Then you will need to do
more than just mutate on the sreen one residue with Pymol.
Jürgen
On 2 Dec 2008, at 17:29, Hongmin Zhang wrote:
Dear All,
I am trying to mutate a single amino acid in a PDB to see
if the mutant
disturbs ligand binding. Does anyone know any software that
can do such work?
Thanks a lot!
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
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Jürgen Bosch
University of Washington
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Phone: +1-206-616-4510
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