<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:Courier New,courier,monaco,monospace,sans-serif;font-size:10pt"><div style="font-family: Courier New,monaco,monospace,sans-serif; font-size: 8pt;">Hi Tim,<br><br>
> Is there an easy way to specify unwanted cis-peptides and<br>> remove them in refinement or with torsion dynamics or SA?<br><br>You can remove dihedral restraints like this:<br><br> refinement.geometry_restraints.remove {<br> dihedrals = chain A and ((resid 100 and (name CA or name C)) or (resid 101 and (name N or name CA)))<br> }<br><br>Although it will remove all dihedrals that somehow involve the selected<br>atoms, which may not be what you want.<br><br>You can also change<br><br> refinement.pdb_interpretation.peptide_link.cis_threshold=10<br><br>(the default is 45 degrees); this will lead to trans restraints.<br><br>If this doesn't help, could you describe more what you want to do?<br><br>Ralf<br><br></div>
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