After outputting the hydrogens, delete the ones you don't want and from
then on do refinement with:
make hout Y
make hydr Y
When you do that, refmac will keep the hydrogens you put in, and also
put them in the output.
-James Holton
MAD Scientist
On 3/29/2018 2:11 PM, Phil Jeffrey wrote:
> I've got a couple of instances where I have non-standard amino acids,
> nevertheless present in the monomer dictionary, that have additional
> non-peptide covalent linkages. I've figured out how to define these,
> but if I opt to output hydrogens as a diagnostic I see that Refmac
> doesn't delete the ligand hydrogens that were present at the linkage
> point.
>
> Nothing catastrophic happens in refinement but extra atoms lying along
> other covalent bonds makes me a little queasy.
>
> Is there something (non-obvious) in additional user-defined .cif
> library that I can use to do this ? Do I simply define a new version
> of the monomer (w/o errant hydrogen) and hope that it overwrites the
> previous definition ?
>
> I'm doing this at borderline atomic resolution.
>
> Thanks
> Phil Jeffrey
> Princeton
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