Hello Mark, I absolutely agree with this. The worst thing is when everybody is following their own personal rules, and there are no major guidelines for end-users to figure out how to interpret those parts. I assume there are no absolute guidelines simply because there isn't any consensus among crystallographers... (from what we can gather from this set of emails...). On the other hand, this discussion has flared up many times in the past, and maybe it's time for a powerful dictator at the PDB to create the law...
Filip Van Petegem On Wed, Mar 30, 2011 at 8:37 AM, Mark J van Raaij <[email protected]>wrote: > 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 > -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: [email protected] http://crg.ubc.ca/VanPetegem/
