> I guess I missed it in the flurry of replies to this thread over the > last few days, but what exactly is so terrible about keeping the atoms > (since you have chemical evidence from protein sequence that they are > there, and even if there is X-ray damage they were originally there and > are likely still there in a subset of the molecules), but changing > occupancy to zero as an acknowledgment that your data does not provide > evidence to support a specific atomic position for these atoms?
Some users might pull up the structure, see those atoms, and think their positions were based on data, which they were not, and then draw conclusions based on them. I agree that occ=0 is tantamount to the suggestion you queried, however. A somewhat key question might be: across the various molecular visualization programs, what is the default way to handle atoms with occ=0? Perhaps those programs might be the best place to fix the problem... JPK ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: [email protected] *******************************************
