On Tue, 18 Apr 2006, Nimira Ulberich wrote: > Hi Xplorers, > > When trying to add unknown atoms to Cyana output PDBs for Xplor use, > like HT2/HT3, OT2, or Histidine HD1 or HE2, I noticed coordinates of > the patched atoms are funny (visually not in position) in some, if not > all, of the PDB files. This makes me wondering how robust is the > method implemented in protocol.addUnknownAtoms.
I had a similar problem - I was taking a protein structure calculated in cyana into xplor. I then attached some post-translational modifications in xplor using addUnknownAtoms. Charles Schwieters suggested a call to protocol.fixupCovalentGeom() afterwards. That might help you For protons, you might be able to get away with using hbuild. If you are interested, I can send you my script, though it is somewhat specialized. Best of luck, -Greg Zornetzer [email protected]
