Dear ccp4bb, I am having an issue with a non-standard amino acid in Coot. I have a cyclic peptide that is stapled using two cysteine residues and a methylene bridge. I have prepared a restraints file using ACEDRG for a methyl cysteine as a surrogate for one of the cysteine residues and I have fitted it into the density in the appropriate space within the peptide where the cysteine would have been. I have made LINKs between the appropriate atoms of the previous and subsequent amino acids in the peptide chain to the methyl cysteine, as well as between the methyl component of the methyl cysteine and the bonded cysteine residue to form a methylene bridge. The resulting pdb file runs without fault within REFMAC, but when I open the refined files in Coot and try to triple refine the methyl cysteine within the peptide chain Coot pushes all the residues away from each other.
Please can someone advise as to what I am missing/doing wrong! Many thanks in advance, Gareth ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
