Dear K, I do think there is much of a hornet's nest to be stirred up by your questions. I hate to advertise it, but chapter 12 of BMC has a thorough discussion of the subject.
Ad riding: ADDING riding hydrogens is not exactly the same as MODELLING some stuff one has no clue about (like parts with no density). Covalently bonded hydrogens are not really 'modeled' in a sense of parameterization, they are almost certainly there, and add no parameters to a model. They just make certain computations of restraints and validation work better when included. Propositions about other non-H parts not visible in density, are an entirely different beast. The crystal is made of trillions of molecules, which when they have almost identical conformation in almost all the scattering molecules will show distinct density. So if no density is visible, what are you modeling? One possible conformation of many? The most probable of the non-evidence-bearing ones? Much better to fess up and leave the residues/atoms out of the model. Increased B should be in any case a result of refinement and not arbitrarily set (and let's not go into details of B-restrains which I believe are to this date a challenge to properly implement) while adjusting occupancy is not an option for a main chain. In addition, setting occupancy to 0 for conjured parts is bad because most display programs and users will ignore that column. In practice (as theory) omitting parts that have no density = high B exponential = negligible contribution to scattering factor rarely has a significant effect on refinement parameters, but the model with absent parts is a more truthful, parsimonious model. BR -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of SIPPEL,KATHERINE H Sent: Tuesday, April 13, 2010 5:40 PM To: [email protected] Subject: [ccp4bb] To model or not to model... Dear Crystallographic Community, Dr. Holton made a comment today that got me thinking on the issue of modeling. This has been a hotly debated topic in our own lab but I would like to hear the current opinions of the community as a whole. It is a question of two parts. First, what do you think about modeling into regions of poor density? Do you (A) model something in as best you can while conforming to ideal geometry/chemistry with full disclosure about b-factors in the region, (B) reduce the occupancies of the poorly modeled loops/side chains, or (C) truncate your model, removing loops and side chains from the model at the cost of statistical numbers? From a crystallographers point of view we can assess the quality of the model and make informed decisions as to what conclusions to draw, however most of the greater scientific community has no way to judge this. They do not know what a b-factor is or where to look for an occupancy. Are we doing a disservice to science by emphasizing the minimization of Rwork and Rfree over full disclosure of what we can legitimately see? Secondly, on a similar vein, what is the community's opinion on modeling hydrogens? I have read a lot on the subject and can see both sides of the argument. From a crystallographer's point of view these are very helpful in maintaining geometry and ensuring the model makes chemical sense. I can also see the necessity of submitting them to the pdb so that the statistics can be recreated. On the other hand most biologist has no comprehension of the concept of riding hydrogens. They assume that if the hydrogen is in the pdb, that the crystallographer saw it and use that information to develop experiments. I realize that I may be kicking a hornet nest here but I would genuinely like to know what people think. Thanks, Katherine Sippel SIPPEL,KATHERINE H Ph. D. candidate Department of Biochemistry and Molecular Biology College of Medicine University of Florida
