On 17/05/2016 15:52, wtempel wrote:
>
> is it only my perception that COOT handles real-space refinement of
> Xxx-Pro peptide bonds,(specifically cis peptides?) less gracefully than
> in the past?
It handles it differently, well spotted.
If you had a decent or good map and a model that was trans (and it
should be cis) [1] then Coot will now have additional restraints to keep
it trans that will thwart you. Now you need to explicitly use the Cis
<-> Trans tool to fix the problem (and then refine).
Why? Because (it seemed to me) that unintentional trans->cis conversion
was far more problematic than easy intentional trans->cis was useful.
[1] If you ever did it, my validation tutorial had such a case and
"solved" the problem beautifully.
Paul.
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