[phenixbb] what to do with disordered side chains

Huanwang Yang hyang at rcsb.rutgers.edu
Thu Mar 31 06:32:10 PDT 2011

If a part of sequence has no density, this part will be cut from 
If the side chain of a residue is  lack of density, the opinion is not 
What about the ligand, if no density is observed?


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.

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