Thanks, Sabine. You are right. There was a mistake in my cif file in the line of the peptide definition. I corrected it and now it is fine.
-- Jianghai On Nov 23, 2011, at 11:10 AM, Sabine Schneider wrote: > Hi Jianghai, > > check if the D-Phe is defined as peptide in the cif file > > like for instance in alanine: > > 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 > ALA ALA 'ALANINE ' L-peptide 10 5 > . > # > > Sabine > > > On 11/23/2011 05:04 PM, Jianghai Zhu wrote: >> 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). >>> >
