If a part of sequence has no density, this part will be cut from coordinates. If the side chain of a residue is lack of density, the opinion is not converged. What about the ligand, if no density is observed? Huanwang Ed Pozharski wrote:
The results of the online survey on what to do with disordered side chains (from total of 240 responses):
Delete the atoms 43% Let refinement take care of it by inflating B-factors 41% Set occupancy to zero 12% Other 4%
"Other" suggestions were:
- Place atoms in most likely spot based on rotomer and contacts and indicate high positional sigmas on ATMSIG records - To invent refinement that will spread this residues over many rotamers as this is what actually happened - Delet the atoms but retain the original amino acid name - choose the most common rotamer (B-factors don't "inflate", they just rise slightly) - Depends. if the disordered region is unteresting, delete atoms. Otherwise, try to model it in one or more disordered model (and then state it clearly in the pdb file) - In case that no density is in the map, model several conformations of the missing segment and insert it into the PDB file with zero occupancies. It is equivalent what the NMR people do. - Model it in and compare the MD simulations with SAXS - I would assumne Dale Tronrod suggestion the best. Sigatm labels. - Let the refinement inflate B-factors, then set occupancy to zero in the last round.
Thanks to all for participation,
Ed.