From: Francesco Pietra (
Date: Wed May 04 2011 - 02:45:21 CDT

Solved by adding hydrogens with CHIMERA, which did the stereochemistry
correctly but failed to add one of the hydrogen atoms. I added this
missing hydrogen with Molefacture, which also required inverting
chirality (or forcing tetrahedral, i can't remember). Then, i inserted
the Molefacture-saved pdb for this CH group into the chimera pdb and
saved the whole with vmd.

---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Wed, May 4, 2011 at 8:33 AM
Subject: vmd-l: molefacture "force tetrahedral" failure

i am trying to add the non-polar hydrogens to a marine metabolite pdb.

Problems in adding H to bare methyl groups, be them at a methyl ester
chain C(O)-O-C or at isopropyl group -CHCC. The umbrella of the three
hydrogens added to C (C(O)-O-CH3) is built toward the oxygen atom. As
to the i-prop, -CH(CH3)(CH3) one of the two methyls comes out correct,
the other one with inverted umbrella, as described for the methyl

H addition follows the spatial direction of the initial violet
elongations: if this is incorrect, i found no way to remedy it. "force
tetrahedral" (in order to invert the umbrella), while picking on
either the methyl carbon, or the latter plus the three hydrogen atoms,
or at any intermediate stage of the H addition, does not move

I could replace the three H with different groups, for example H, F,
D, in order to use "invert chirality" but there should be something
simpler and I am simply misusing molefacture. Or this is a situation
that deceits molefacture.

thanks for advice
francesco pietra