Hi Jonathan,
send me files off list and I will have a look. From your description it
isn't clear to me what the problem is. You need to add H or D or H and D
only once (and phenix.ready_set is the right tool to do it!), then just do
refinement and all should work. Coot indeed may not play well with some of
exotic scenarios but so far that hasn't been a huge issue as phenix.refine
can handle this mostly automatically.
Pavel
On Thu, Jun 20, 2019 at 5:44 PM Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
> I am trying to refine a neutron structure for someone and I have come
> across a couple of things which I need help with.
>
> I am struggling to get the occupancy refinement of the
> hydrogens/deuteriums on the N-terminal nitrogens to behave right. Some of
> them get deleted by readyset but the trick seems to be to call them
> hydrogen in the atom name field yet say they are D in the element symbol
> field. Is that the best way? Also, readyset seems to delete the D's in D2O?
>
> I would appreciate any tips on what is the best 'strategy' for refining
> with neutron data i.e. reciprocal- versus real-space or both, etc, because
> my R-free just seems to go up.
>
> Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it
> stretches the O-D bond length from around 1 to 1.3 Angstrom and the bond
> angle from ~110 to about 120 degrees so it seems to be picking-up wrong
> geometry info from somewhere.
>
> --
>
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