On 22/11/11 23:25, Jianghai Zhu wrote:
I am building a cyclic peptide with a D amino acid in the middle. First, how
can I connect the N and C termini of the peptide and make it a peptide bond?
There is no way (in Coot) at the moment, sorry. This is something I am
working on [1]. If you make a link between them, Coot will draw a link
- but that is not (all) that you want (AFAICS).
Second, how do I make the PHE to a D amino acid? I know there is a library of
D-Phenylalanine in mon_lib.cif, but the code for that is PHE-D? I cannot use 5
letters for the residure, can I?
As I suspect you know, several D amino acids have specific three-letter
codes, but D-PHE does not. Using a PDB file, Coot will not detect that
you mean PHE-D and not PHE for the restraints. If you use mmCIF/pdbx
then I think it will work.
Paul.
[1] this is related to carbohydrate refinement and involves using LINKR
information (but I am having trouble extracting that using the current
mmdb libs - I'll poke Eugene about it again).
