On 25/11/2020 03:24, Cheng Zhang wrote:
This question must have been asked before
Correct.
but I couldn't find a good answer online.
the jiscmail archive is a terrible system for archiving our collective knowledge. There should be a better way.
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.
a LINK is necessary but not sufficient.
My question is, how to refine such a modified residue in real space without breaking the covalent bond?
This is not a modified residue. A modified residue would require a different approach. This is a linked residue.
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?
One would do that one step at a time rather than combined, so the answer to that question may be yes or no. You may not need to do step 1 because the residue/compound to which the SER is attached may already be in the monomer library.
Also, let's say there is an unnatural amino acid in the protein, how to define this residue so COOT or Phenix
Depending on the nature of the unnatural amino acid, this may not need any work at all (it may already exist and all you need to do is Replace Residue). But a SER linked to a lipid is not such a case.
can recognize it as an amino acid and the peptide bond restraints still apply to it?
Pyrogen does this (FWIW), but I am not sure if Acedrg does. Anyway, here's a worked example of linking a monomer that already exists in the dictionary (PLP) to a LYS: https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html Paul. ######################################################################## 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/
