I completely agree, although if the IUCr or PDB decides otherwise, I'd be happy to oblige.
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 20:48, Quyen Hoang wrote: > I don't have strong preference either way, but if one has good density for > backbone and no density for a corresponding side-chain, would it be > reasonable to believe that the side-chain might actually exists and that it > has no visible density at a certain contour level might be because it was > moving around (or static disorder)? And if B-factor is an estimate of > thermo-motion (or static disorder), then would it not be reasonable to accept > that building the side-chain and let B-factor sky rocket might reflect > reality more so than not building it? > > Cheers, > Quyen > _______________________________ > Quyen Hoang, Ph.D > Assistant Professor > Department of Biochemistry and Molecular Biology, > Stark Neurosciences Research Institute > Indiana University School of Medicine > 635 Barnhill Drive, Room MS0013D > Indianapolis, Indiana 46202-5122 > > Phone: 317-274-4371 > Fax: 317-274-4686 > email: [email protected] > Website: www.hoanglab.com > > > > On Mar 30, 2011, at 2:04 PM, James Holton wrote: > >> >> I'm afraid this is not a problem that can be solved by "standardization". >> >> Fundamentally, if you are a scientist who has collected some data (be it >> diffraction spot intensities, cell counts, or substrate concentration vs >> time), and you have built a "model" to explain that data (be it a >> constellation of atoms in a unit cell, exponential population growth, or a >> microscopic reaction mechanism), I think it is generally expected that your >> model explain the data "to within experimental error". Unfortunately, this >> is never the case in macromolecular crystallography, where the model-data >> disagreement (Fobs-Fcalc) is ~4-5x bigger than the "error bars" (sigma(F)). >> >> Now, there is nothing shameful about an incomplete model, especially when >> thousands of very intelligent people working over half a century have not >> been able to come up with a better way to build one. In fact, perhaps a >> better name for the "disordered side chain problem" would be "dark density"? >> This name would place it properly amongst "dark matter", "dark energy" and >> other fudge factors introduced to try and explain why our "standard model" >> is not consistent with observation? That is, "dark density" is the stuff we >> can't see, but nonetheless must be there somewhere. >> >> Whatever it is, I personally do hold a vain belief that perhaps someday soon >> the problem of "dark density" will be solved, and that presently instituting >> a "policy" requiring that all macromolecular models from this day forward >> remain at least as incomplete as yesterday's models is not a very good idea. >> I say: if you think there is "something there" then you should build it in, >> especially if it is important to the conclusions you are trying to make. >> You can defend your model the same way you would defend any other scientific >> model: by using established statistics to show that it agrees with the data >> better than an "alternative model" (like leaving it out). It is YOUR model, >> after all! Only you are responsible for how "right" it is. >> >> I do appreciate that students and other novices may have a harder time >> defining "surfaces" and measuring hydrogen bond lengths in these pesky >> "floppy regions", but perhaps their education would be served better by >> learning the truth sooner than later? >> >> -James Holton >> MAD Scientist >> >> >> On 3/30/2011 9:26 AM, Filip Van Petegem wrote: >>> 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/ >> >
