Hello, it depends a bit on the resolution. With d<1.2 A you can, of course, do some quite complicated modelling of alternate confirmations, group occupancies, etc - actually you can do this very meaningfully at worse resolutions, too. My favourite subject - if your resolution is better than ~1.4 to 1.6 A, you can often clean up the difference map by refining anisotropic B's. Otherwise (my opinion is that) it's best not to do anything too complicated so just letting the B-factors go a bit high seems the best way! What side chains are we talking about - Cys, Met? I am not an expert on radiation damage but about 20 years ago the discussion was that the more exotic damage e.g. to carboxyl groups, requires much bigger doses than one would use for normal data collection, but nowadays that may be not be true. It would be interesting to know.
Jon Cooper
On 28 Apr 2020 16:37, "Thomas, Leonard M." <lmtho...@ou.edu> wrote:
Hello all,
This is one of those issues that seems to come up now and then. I have been working on a structure that obviously has some radiation damage as indicted by negative density and/or high thermal parameters. Since we know that residue X is in the sequence the sidechain should be there and is just flopping around or has been damaged/removed by radiation exposure. My questions is what is the current thinking on presenting these residues for deposition. Remove the side chain atoms, drop the occupancy to zero, just let them behave as they want ie high B factors some negative density.
Cheers,Len
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