On Sun, Jan 30, 2011 at 8:26 AM, Timothy Springer
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