What about setting both the occupancy to 0 *and* setting the b-factors to some special arbitrary number, say, 500? Then people would pick up easily on the side chains being dubious, and the refinement would not be affected by them.
Jacob On Wed, Mar 30, 2011 at 10:29 AM, Phoebe Rice <pr...@uchicago.edu> wrote: > 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 > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *******************************************
