I agree with Zbyszek with the modeling of side chains and stress the following points:
1) It drives me nuts when I find that PDB is missing atoms from side chains. This requires me to rebuild them to get any use out of the PDB such as relevant surface renderings or electropotential plots. I am an experienced structural biologist so that I can immediately identify that they have been removed and can rebuild them. I feel sorry for my fellow scientists from other biological fields that can't perform this task readability, thus removing these atoms from a model limits their usefulness to a wider scientific audience. 2) Not sure if any one has documented the percentage of actual side chains missing from radiation damage versus heterogeneity in confirmation (i.e. dissolved a crystal after collection and sent it to Mass Spec). Although the former likely happens occasionally, my gut tells me that the latter is significantly more predominant. As a result, absence of atoms from a side chain in the PDB where the main chain is clearly visible in the electron density might make for the best statistics for an experimental model, but does not reflect a reality. Scott On Thu, Mar 31, 2011 at 4:43 PM, Zbyszek Otwinowski <zbys...@work.swmed.edu>wrote: > Regarding the closing statement about the best solution to poorly ordered > side chains: > > I described in the previous e-mail the probabilistic interpretation of > B-factors. In the case of very high uncertainty = poorly ordered side > chains, I prefer to deposit the conformer representing maximum a posteriori, > even if it does not represent all possible conformations. > Maximum a posteriori will have significant contribution from the most > probable conformation of side chain (prior knowledge) and should not > conflict with likelihood (electron density map). > Thus, in practice I model the most probable conformation as long as it it > in even very weak electron density, does not overlap significantly with > negative difference electron density and do not clash with other residues. > > As a user of PDB files I much prefer the simplest and the most informative > representation of the result. Removing parts of side chains that carry > charges, as already mentioned, is not particularly helpful for the > downstream uses. NMR-like deposits are not among my favorites, either. > Having multiple conformations with low occupancies increases potential for a > confusion, while benefits are not clear to me. > > Zbyszek > > Frank von Delft wrote: > >> This is a lovely summary, and we should make our students read it. - But >> I'm afraid I do not see how it supports the closing statement in the last >> paragraph... phx. >> >> >> On 31/03/2011 17:06, Zbyszek Otwinowski wrote: >> >>> The B-factor in crystallography represents the convolution (sum) of two >>> types of uncertainties about the atom (electron cloud) position: >>> >>> 1) dispersion of atom positions in crystal lattice >>> 2) uncertainty of the experimenter's knowledge about the atom position. >>> >>> In general, uncertainty needs not to be described by Gaussian function. >>> However, communicating uncertainty using the second moment of its >>> distribution is a widely accepted practice, with frequently implied >>> meaning that it corresponds to a Gaussian probability function. B-factor >>> is simply a scaled (by 8 times pi squared) second moment of uncertainty >>> distribution. >>> >>> In the previous, long thread, confusion was generated by the additional >>> assumption that B-factor also corresponds to a Gaussian probability >>> distribution and not just to a second moment of any probability >>> distribution. Crystallographic literature often implies the Gaussian >>> shape, so there is some justification for such an interpretation, where >>> the more complex probability distribution is represented by the sum of >>> displaced Gaussians, where the area under each Gaussian component >>> corresponds to the occupancy of an alternative conformation. >>> >>> For data with a typical resolution for macromolecular crystallography, >>> such multi-Gaussian description of the atom position's uncertainty is not >>> practical, as it would lead to instability in the refinement and/or >>> overfitting. Due to this, a simplified description of the atom's position >>> uncertainty by just the second moment of probability distribution is the >>> right approach. For this reason, the PDB format is highly suitable for >>> the >>> description of positional uncertainties, the only difference with other >>> fields being the unusual form of squaring and then scaling up the >>> standard >>> uncertainty. As this calculation can be easily inverted, there is no loss >>> of information. However, in teaching one should probably stress more this >>> unusual form of presenting the standard deviation. >>> >>> A separate issue is the use of restraints on B-factor values, a subject >>> that probably needs a longer discussion. >>> >>> With respect to the previous thread, representing poorly-ordered (so >>> called 'disordered') side chains by the most likely conformer with >>> appropriately high B-factors is fully justifiable, and currently is >>> probably the best solution to a difficult problem. >>> >>> Zbyszek Otwinowski >>> >>> >>> >>> - 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. >>>>>> >>>>> But this "knowledge" may be quite wrong. If the flaming red really >>>>> indicates >>>>> large vibrational motion then yes, one whould not bet on stable >>>>> H-bonds. >>>>> But if the flaming red indicates that a well-ordered sidechain was >>>>> incorrectly >>>>> modeled at full occupancy when in fact it is only present at >>>>> half-occupancy >>>>> then no, the H-bond could be strong but only present in that >>>>> half-occupancy >>>>> conformation. One presumes that the other half-occupancy location >>>>> (perhaps >>>>> missing from the model) would have its own H-bonding network. >>>>> >>>>> I beg to differ. If a side chain has 2 or more positions, one should >>>> be a >>>> bit careful about making firm conclusions based on only one of those, >>>> even >>>> if it isn't clear exactly why one should use caution. Also, isn't the >>>> isotropic B we fit at "medium" resolution more of a "spherical cow" >>>> approximation to physical reality anyway? >>>> >>>> Phoebe >>>> >>>> >>>> >>>> >>> Zbyszek Otwinowski >>> UT Southwestern Medical Center at Dallas >>> 5323 Harry Hines Blvd. >>> Dallas, TX 75390-8816 >>> Tel. 214-645-6385 >>> Fax. 214-645-6353 >>> >> >> > > -- > Zbyszek Otwinowski > UT Southwestern Medical Center > 5323 Harry Hines Blvd., Dallas, TX 75390-8816 > (214) 645 6385 (phone) (214) 645 6353 (fax) > zbys...@work.swmed.edu > -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry & Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
