[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.

thanks,
Nat



More information about the phenixbb mailing list