On May 4, 2011, at 10:05 AM, Francesco Pietra wrote:
Hello: i had partial failure in addH to a natural product. H at a quaternary, chiral C was not added in spite of repeated attempts.
Hi Francesco, My guess is that Chimera does not believe that the problem carbon is sp3, which Chimera decides based on the carbon's bond geometry. You can see what atom type Chimera assigned to that carbon by selecting it and then doing Actions->Label->IDATM type. An sp3 carbon would be "C3". An sp2 carbon would be "C2". A full table of atom types is here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/idatm.html You can force Chimera to believe the carbon is sp3 by selecting it and then using this command: setattr a idatmType C3 sel It would also probably be helpful if you used Help->Report A Bug to submit a bug report on this problem, attaching the structure file. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
All Hs were added by my favorite drawer (for organic compounds); however, this changes the coordinates, which is not what I want.
I solved the issue by transferring the chimera pdb output to vmd, adding the missing H with Molefacture.
On the other hand, Molefacture, if asked to add all Hs, resulted in incorrect stereochemistry at -O-CH3 and some -C-CH3 (inverted umbrella, which could not be reversed).
francesco pietra _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users