I've now polled 4 fairly savvy "end users" of crystal structures and there seems to be a consensus:
- they all know what B is and how to look for regions of high B (with, say, pymol) and they know not to make firm conclusions about H-bonds to flaming red side chains. - None of them would ever think to look at occupancy and they don't know how anyway. - they expect that loops with disordered backbones would not be included in the models, and can figure out truncated or fake-ala side chains with some additioanl effort, but that option makes viewing surfaces and e-stats more of a pain. Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp ---- Original message ---- >Date: Tue, 29 Mar 2011 17:43:49 -0400 >From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf of Ed Pozharski ><epozh...@umaryland.edu>) >Subject: [ccp4bb] what to do with disordered side chains >To: CCP4BB@JISCMAIL.AC.UK > >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
