[phenixbb] cis peptides

Timothy Springer springer at idi.harvard.edu
Sun Jan 30 13:57:01 PST 2011

I notice that during manual rebuilding cis peptides are frequently put in by mistake. It is considerable manual work to make them trans and would be nice to follow that with torsion dynamics with say a 3.1 A structure we    are working on. Coot can find a list of cis peptides and it is often a surprise to postdocs to see it. I will ask mehmet to send you structure and list of the non-pro ones. 

Sent from my iPhone

On Jan 30, 2011, at 12:52 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Sun, Jan 30, 2011 at 8:26 AM, Timothy Springer
> <springer at idi.harvard.edu> wrote:
>> Is there an easy way to specify unwanted cis-peptides and remove them in refinement or with torsion dynamics or SA?
> Aside from Ralf's suggestions, there isn't currently a way to do this
> explicitly.  My understanding is that SA (torsion or Cartesian)
> usually isn't sufficient to rotate a peptide 180 degrees, although I
> guess it's worth a try.  However, I'm working on code to automatically
> correct misfit peptides, and it wouldn't be difficult to specifically
> handle cis-peptides, and to accept an explicit atom selection instead
> of looping over all residues.  (It's only semi-functional right now -
> it runs, but doesn't always improve the model; fixing it is on my
> agenda for the coming week.)  If you're willing to share the model and
> data that you're concerned about, it might speed up my testing.
> thanks,
> Nat
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