perhaps the IUCr and/or PDB (Gerard K?) should issue some guidelines along these lines? And oblige us all to follow them? Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1
On 30 Mar 2011, at 17:29, Phoebe Rice 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 <[email protected]> (on behalf of Ed Pozharski >> <[email protected]>) >> Subject: [ccp4bb] what to do with disordered side chains >> To: [email protected] >> >> 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
