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Thanks the CCP4 bulletin board for interesting and helpful discussions like this. Personally, I think either inflating B-factors of the sidechain or putting occupancy at zero is acceptable. The latter is stricter and scientifically sound, but also harder to handle. How do you define visible and non-visible? I am sure that at certain signal/noise ratio, you are going to see something on the density map? The concern is actually how not to confuse the regular users of our structures. It is not helpful that there are several approaches to treat the same problem and even we crystallographers don't agree with each other. It is up to PDB and the program developers or some other organizations to come up with a standard way. Pick one of the options above or invent something new. It doesn't have to be the perfect option. But, it would be much easier to educate non-crystallographers how to notice disordered regions and for visualization programs to give warning notes to their users. By the way, the thread started with the question about Lys sidechain on the surface. How many of you think the conformation of it could actually help interpret biological phenomena? Isn't it supposed to be flexible in solution? Even if we have clear densities for it at high resolution, it is likely just stabilized by other partners in the crystal and thus artificial, right? Rui
