Dear Ed, Thankyou for this and apologies for late reply. If one has chemical evidence for the presence of residues but these residues are disordered I find the delete atoms option disagreeable. Such a static disorder situation should be described by a high atomic displacement parameter, in my view. (nb the use of ADP is better than B factor terminology). Yours sincerely, John Prof John R Helliwell DSc
On 29 Mar 2011, at 22:43, Ed Pozharski <epozh...@umaryland.edu> 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. > > -- > "I'd jump in myself, if I weren't so good at whistling." > Julian, King of Lemurs
