Hi Pavel,
To define a weak bond, would you use "geometry_restraints.edits { ... bond
{... " , and just set a rough distance_ideal and a very high sigma (like
say 5A)?
Or are you referring to something different?
Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide
On Tue, Dec 20, 2016 at 1:28 PM, Pavel Afonine <[email protected]> wrote:
> Hi Andrew,
>
> you can define a weak bond between clashing atoms which will disable
> repulsion. A weak bond should not introduce any bias.
>
> Pavel
>
> On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall <
> [email protected]> wrote:
>
>> 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
>>
>>
>
