On Wed, 2011-03-23 at 14:39 -0700, Pavel Afonine wrote:
Some people tend to chop them off (which I do not not not like), some let the refinement programs do what they want, and the programs stupidly tends to stick these sidechains in whatever density is available around (this is bad too).
Yes, there are basically three options: 1) cut the side chain down to whatever is still visible in the density 2) let the refinement proceed as is 3) set side chain atom occupancies to zero Personally, I have evolved from 2) to 1). The argument was that omitting atoms will confuse some end users, and refinement will essentially take care of it by increasing the B-factors. I have seen some quite convincing evidence since that the disordered side chains do have a detectable effect on the rest of the model, and thus leaving them in makes a model worse. Other half of the argument was of semantic nature and referred more to replacing disordered residues with alanines, which is silly because we know from sequence it's not alanine and we know the atoms must be in the vicinity. But on the other hand we exclude whole segments of sequence sometimes, such as disordered loops and termini, so why not side chains? Missing atoms are just that - missing from the density. Chemically it is still a lysine, according to the residue name. The third option (the one you gravitate towards) seems problematic to me for the following reasons. The meaning of the occupancy is that the atom distribution in space is multimodal, and it spends certain fraction of time vibrating around the specified position. So what is the meaning of zero occupancy? This is the average atomic position, but it spends zero time here? Makes no physical sense, and in fact is wrong since there is some non-zero probability that the disordered side chain will occupy the designated conformation. Of course, structural model may be considered a *mathematical* model, and it does not have to be strictly interpretable (or interpretable the way I see most logical, anyway). As for end-user argument, I would say that omitted atoms are better than high B-factors or zero occupancies, as it is more likely to attract attention to the fact that side chain conformation is undefined (coot, however, does highlight zero occupancy atoms). It is true though that the "end-user argument" is inherently weak, since nobody can be held responsible for self-inflicted damage due to lack of knowledge. Except MacDonalds and microwave oven manufacturers, of course. -- Hurry up, before we all come back to our senses! Julian, King of Lemurs