All-
I have been attempting to add atoms to proteins that are missing
electron density, mostly surface positions. In most cases I have been
able to just add an atom or two (Build->Fragment->group); sometimes
adding a whole rotamer is required. I have been unable to add a planar
guanidino group or the planar oxygens to Asp or Glu. How would I change
hybridization of atoms to get the correct geometry?
Also, where are the rotamers in pymol from? Are they backbone dependent
or independent? How hard would it be to use a different set of rotamers?
Thanks.
Eric
