Why not have the "b-factors take care of it" until some magic cutoff number? When they reach the cutoff, two things happen:
1. Occupancies are set to zero for those side chains, to represent our lack of ability to model the region, 2. B-factors are set to exactly 500, as a "flag" allowing casual b-factor-savvy users to identify suspicious regions, since they will probably not see occupancies, but *will* see b-factors. Therefore, all 0-occupancy atoms will automatically have b-factors = 500. I believe it is true that if the occupancies are zero, the b-factors are totally irrelevant for all calculations? Doesn't this satisfy both parties? Jacob On Thu, Mar 31, 2011 at 9:22 AM, <herman.schreu...@sanofi-aventis.com> wrote: > Dear Quyen, > I am afraid you won't get any better answers than you got so far. There is > no holy bible telling you what to do with disordered side chains. I fully > agree with James that you should try to get the best possible model, which > best explains your data and that will be your decision. Here are my 2 cents: > > -If you see alternative positions, you have to build them. > -If you do not see alternative positions, I would not replace one fantasy > (some call it most likely) orientation with 2 or 3 fantasy orientations. > -I personally belong to the "let the B-factors take care of it" camp, but > that is my personal opinion. Leaving side chains out could lead to > misinterpretations by slightly less savy users of our data, especially when > charge distributions are being studied. Besides, we know (almost) for sure > that the side chain is there, it is only disordered and as we just learned, > even slightly less savy users know what flaming red side chains mean. Even > if they may not be mathematically entirely correct, huge B-factors clearly > indicate that there is disorder involved. > -I would not let occupancies take up the slack since even very savy users > have never heard of them and again, the side chain is fully occupied, only > disordered. Of course if you build alternate positions, you have to divede > the occupancies amongst them. > > Best, > Herman > > ________________________________ > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Quyen > Hoang > Sent: Thursday, March 31, 2011 3:55 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] what to do with disordered side chains > > We are getting off topic a little bit. > Original topic: is it better to not build disordered sidechains or build > them and let B-factors take care of it? > Ed's poll got almost a 50:50 split. > Question still unanswered. > Second topic introduced by Pavel: "Your B-factors are valid within a > harmonic (small) approximation of atomic vibrations. Larger scale motions > you are talking about go beyond the harmonic approximation, and using the > B-factor to model them is abusing the corresponding mathematical model." > And that these large scale motions (disorders) are better represented by > "alternative conformations and associated with them occupancies". > My question is, how many people here do this? > If you're currently doing what Pavel suggested here, how do you decide where > to keep the upper limit of B-factors and what the occupancies are for each > atom (data with resolution of 2.0A or worse)? I mean, do you cap the > B-factor at a reasonable number to represent natural atomic vibrations > (which is very small as Pavel pointed out) and then let the occupancies pick > up the slack? More importantly, what is your reason for doing this? > Cheers and thanks for your contribution, > Quyen > > On Mar 30, 2011, at 5:20 PM, Pavel Afonine wrote: > > Mark, > alternative conformations and associated with them occupancies are to > describe the larger scale disorder (the one that goes beyond the B-factor's > capability to cope with). > Multi-model PDB files is another option. > Best, > Pavel. > > > On Wed, Mar 30, 2011 at 2:15 PM, VAN RAAIJ , MARK JOHAN > <mjvanra...@cnb.csic.es> wrote: >> >> yet, apart from (and additionally to) modelling two conformations of the >> side-chain, the B-factor is the only tool we have (now). >> Quoting Pavel Afonine: >> >> > Hi Quyen, >> > >> > >> > (...) 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? >> >> >> > >> > NO. Your B-factors are valid within a harmonic (small) approximation of >> > atomic vibrations. Larger scale motions you are talking about go beyond >> > the >> > harmonic approximation, and using the B-factor to model them is abusing >> > the >> > corresponding mathematical model. >> > http://www.phenix-online.org/newsletter/CCN_2010_07.pdf >> > >> > Pavel. >> > >> >> Mark J van Raaij >> Laboratorio M-4 >> Dpto de Estructura de Macromoléculas >> Centro Nacional de Biotecnología - CSIC >> c/Darwin 3, Campus Cantoblanco >> 28049 Madrid >> tel. 91 585 4616 >> email: mjvanra...@cnb.csic.es > > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *******************************************
