30 Jan
2011
30 Jan
'11
3:06 p.m.
Hi Tim,
Is there an easy way to specify unwanted cis-peptides and remove them in refinement or with torsion dynamics or SA?
You can remove dihedral restraints like this: refinement.geometry_restraints.remove { dihedrals = chain A and ((resid 100 and (name CA or name C)) or (resid 101 and (name N or name CA))) } Although it will remove all dihedrals that somehow involve the selected atoms, which may not be what you want. You can also change refinement.pdb_interpretation.peptide_link.cis_threshold=10 (the default is 45 degrees); this will lead to trans restraints. If this doesn't help, could you describe more what you want to do? Ralf