Judging from some examples in the literature, if there's no density for the ligand, you publish in Nature!
On 31 Mar 2011, at 14:32, Huanwang Yang wrote: > 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. >> >> ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
