On 20/01/15 15:32, ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ wrote:
Dear All,
I wonder if you could help me with this. I am trying to do some
regularisation/real space refinement of a ligand with Coot. The ligand is a
pseudopeptide with two non-standard aminoacids, followed by several standard
ones. I assume that to do this correctly, I would need a cif file that
specifies the two non-standard aa's plus the links between these two and
between second and third (which is a standard one).
What's the group? You need 'peptide'.
When trying to generate a cif with a program such as eLBOW (using a pdb as the
starting reference), each of the non-standard aa's gets a cif of its own, and
the third, standard one, is ignored, meaning that there are no specified links
between the first two (non-standard) and even less between second
(non-standard) and third (standard).
Have you read the JLigand tutorial?
Coot of course keeps each aa as it should be, but breaks up the peptide chain
completely.
When you try to do what?
Could you direct me how to built a cif that includes such bond specifications,
starting from a reference pdb or otherwise? Is there an altogether different
way of getting Coot to do what I want?
You can use Prodrg (via Prodrgify in Coot) but that is not recommended
(because it requires chemistry perception)
I have no reason to doubt that Elbow restraints for modified amino acids
would be just fine. I wouldn't do it that way, of course though.
Paul.
