Dear Len,
maybe a slight side-track, but you could consider taking one step back
and applying a slightly different approach to data-processing -
something we call "F(early)-F(late)" maps in autoPROC [1].
Why could that be useful here? Because it might allow you to
(1) differentiate between radiation damage (atoms present at the
beginning but "lost" or "somewhere else" at the end - which could
be modelled through occupancy refinement) and genuine disorder
(static throughout the experiment - probably best described
through large B-factros);
(2) generate and use a dataset of the least damaged subset of
reflections to refine against;
Note: this is different from just processing a subset of your
images, since all data is still scaled together but merged
separately.
Of course, this all assumes that data were collected on a modern
detector/beamline using a low-dose, high-multiplicity (and
fine-sliced) strategy - but that is nowadays usually the case anyway
due to fast detectors and shutterless collection (and because it
allows for more flexibility and better data in the end).
There are other approaches to this (e.g. zero-dose extrapolation [2]
or RABDAM [3]), but if you have a set of diffraction images sitting on
disk it might be easy to just push them through our software.
If you want to have a look at some recent examples (of what you might
be able to learn about your data, collection strategy or model
refinement) also related to radiation damage:
https://www.globalphasing.com/autoproc/wiki/index.cgi?Covid19
https://www.globalphasing.com/buster/wiki/index.cgi?Covid19
Cheers
Clemens
[1] https://www.globalphasing.com/autoproc/
[2] Diederichs et al (2003). Acta D 59,903-909.
[3] Shelley et al (2018). J Appl. Cryst 51, 552-559.
On Tue, Apr 28, 2020 at 03:37:20PM +0000, Thomas, Leonard M. 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
>
> Leonard Thomas
> [email protected]<mailto:[email protected]>
>
>
>
>
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