Hi Andrew,
The simplest way would be to place the "offending" atoms in separate
conformers as used to refine alternate conformations. This is a 1-letter
code that goes just before the 3-letter residue name:
> ATOM 139 SG *B*CYS A 21 -20.620 4.518 34.501 0.39
> 12.23 A S
This trick should cause PHENIX to ignore close distances between atoms
in the A and B conformers.
Hope this helps,
Pedro Matias
Às 05:39 de 19/12/2016, Andrew Marshall escreveu:
> Hi all,
>
> I have a structure of a condensing enzyme with substrate bound. The
> active site is very tight, requiring some of the substrate atoms to
> clash with a catalytic cysteine. This means that although the
> substrate fits the density nicely upon manual real-space refinement,
> phenix recognises the clash, resulting in the displacement of
> substrate atoms so that they are outside the density. I can mostly fix
> this by using distance restraints, but I'd rather allow it to refine
> in a less biased manner, but ignore the clash. Is this a acceptable
> way forward? If so, is there a parameter I can edit to tell phenix to
> ignore clashes between these specific atoms?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
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