> Indeed, omitting atoms from a model is better than including them at 0 occupancy... It is just that, REMARKS or no REMARKS, people will use the models in the PDB as is, > for example to draw surface plots with electrostatic potential coloring, and then interprete these as if the lysines were truncated at CB. I agree that people will use a PDB file as is - but surely, we, as creators of said PDB file, can steer them away from any potential pitfalls...
If you do not know what a B-value is you cannot use PDB structures in an
opiniated way, coordinates and temp factors cannot be used independent of each other in my
humble opinion.
But surely that's like saying "You can't use SHARP because you can't derive Bayes' Theorem ". We can't expect the end-users of the structural information that we provide to all be as au fait with the structure (and the techniques/caveats associated with it) as those who have slaved away over coot building it. Flip D ------------------------------ *From:* David Briggs [mailto:[EMAIL PROTECTED] *Sent:* Wednesday, January 10, 2007 13:22 *To:* Flip Hoedemaeker *Subject:* Re: [ccp4bb]: Modelling disordered side-chains
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
