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.
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
> 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.
>> On Wed, Dec 3, 2008 at 12:50 PM, Juergen Bosch
>> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>> 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.
>> 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
> 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