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.
...assuming the end-user knows what a B-factor is... If you can't say with certainty that it's there... why detract from the accuracy of your model by including stuff that isn't in the data. you are artificially increasing the R-factor of your model by making your obs:param ratio less favourable. Altering numbers in a pdb (how many non-structural users check the Occ & B-factor columns regularly) is less transparent. If you remove the atoms, any user will spot the problem, and then (hopefully) read the pdb remarks where (hopefully) you will have a list of missing atoms or a helpful remark stating that any atoms missing are missing because they were not ordered in the structure. D -- --------------------------------------- David Briggs, PhD. Father & Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile -- --------------------------------------- David Briggs, PhD. Father & Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile
