Sorry to make things confusing. After I have the correct peptide definition in my cif file as suggested by Sabine, like the following.
data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level DPH DPH 'D-PHENYLALANINE ' D-peptide 23 12 . COOT is happy to treat DPH as a normal amino acid and doesn't give me the chiral volume warning and tries to make it a L amino acid. COOT did draw a line between my N and C -termini of the cyclic peptide based on the LINK record I added into the pdb file, but wouldn't enforce the distance in the LINK record during regularization. -- Jianghai On Nov 23, 2011, at 11:48 AM, Paul Emsley wrote: > On 23/11/11 16:04, Jianghai Zhu wrote: >> I can take the D-PHE cif out and rename it to DPH. > > Yes... > >> 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. > > To be more precise, Coot does not consider DPH to be a standard amino acid > (it isn't). > >> Any way to circumvent that? >> > > I am a bit confused about what is going on - Coot quite happily draws the N-C > bonds in gramicidins. > > You should get a dotted line for a LINK record if you have such a thing... > > Paul. >
