Hello, I am again struggling with a similar problem and have only (re?-)discovered Paul's May 23 reply today. Thus, I pushed that "<Cis <-> Trans>" button and, yes, I now can still recognize the proline after real-space refinement. But the COOT planar restraints for the cis-peptide appear to be much weaker than for trans-peptides. It almost feels like the "Cis<->Trans" lifts the trans restraints without imposing cis restraints. I have experimented with the "add planar peptide restraints" menu, but did not notice any effect. Am I going about this problem in the "right" COOT way? Best regards. Wolfram
On Mon, May 23, 2016 at 3:28 PM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > 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. > >
