I can take the D-PHE cif out and rename it to DPH. But the peptide bonds at the N and C terminus of DPH are broken in COOT since COOT doesn't consider DPH as an amino acid. Any way to circumvent that? Thanks.
-- Jianghai On Nov 23, 2011, at 7:51 AM, Paul Emsley wrote: > 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). >
