Hello, I think this thread from a few months ago will help. https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2007&L=CCP4BB&D=0&P=49210
Best wishes, Jon Cooper -------- Original Message -------- On 25 Nov 2020, 03:24, Cheng Zhang wrote: > 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 ######################################################################## 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/
