[phenixbb] cis peptides

Nathaniel Echols nechols at lbl.gov
Sun Jan 30 09:52:28 PST 2011

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.


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