Hi everyone, This question must have been asked before but I couldn't find a good answer online.
I work on a cryo-EM structure with one serine residue covalently linked with a lipid molecule. The map for the lipid moiety was there but not good enough to unambiguously place each atom. I tried to manually model the lipid moiety to fit the map. But if I refine it in real space, it would move away from the serine residue even though I linked it to the residue in the PDB file. My question is, how to refine such a modified residue in real space without breaking the covalent bond? Is there any way to make a molecular topology file for the lipid moiety that also contains restraints for the covalent bond with the modified residue? Also, let's say there is an unnatural amino acid in the protein, how to define this residue so COOT or Phenix can recognize it as an amino acid and the peptide bond restraints still apply to it? Thanks! Cheng -- --------------------- Cheng Zhang ######################################################################## 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/
