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On Wed, 10 Jan 2007, Flip Hoedemaeker wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hmm, I'd like to stay as close as possible to the biological "truth"... In > this case, you know that the lysine side chain atoms are there but you just > can't see them! I always leave these atoms in, in a preferred rotamer (with > 1.0 occupancy!) and let the B-values refine to >100. These high B-values > clearly indicate the issue at hand, and you can colour the model > accordingly. > One possibility is indeed to put all possible rotamers coordinates, only I would not recommand 1/Nrot occupancy, but, instead, Boltzmann-like weights with an Energy taking into account both the Corr. coeff. of that particular rotamer in the electron density (E-1-CC) and a penalty given by some oracle called Ms_Bump. Ms_Bump would return a high penalty if sidechain atoms of the rotamer bump into either mainchain or other sidechain atoms. If the sidechain is "there", all occupancies of the rotamers should add up to one. Now, an interesting pb. is how to cwevaluate bumps with sidechains with "multiple copies" (i.e. rotamers) with partial occupancy. The answer is to take a weighted sum of all copies of the other sidechains, ignoring the copies of the same sidechain. The weights should be calculated self-consistently, as described in Koehl and Delarue, 1994, J. Mol. Biol. 329:249-275. Everything can be precalculated (bumps, score in electron density) for each rotamer, so the iterations will be pretty quick. The approach could be generalized to authorize all rotamers of possible aminoacid types to assign sequence in a polyALA backbone. Only the weights are varied, self-consisently. Marc DELARUE, Dynamique Structurale des Macromolecules, URA 2185 du CNRS Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France. Tel : 33 1 45 68 86 05. Fax : 33 1 40 61 37 93 Web : http://lorentz.dynstr.pasteur.fr/website/index.html
