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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: [log in to unmask] 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 <[log in to unmask] >> > 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 <[log in to unmask]> (on behalf of >> Ed Pozharski <[log in to unmask]>) >> >> Subject: [ccp4bb] what to do with disordered side chains >> >> To: [log in to unmask] >> >> >> >> 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: [log in to unmask] >> http://crg.ubc.ca/VanPetegem/ >