Another option for adding hydrogen atoms to pdb files is the excellent Molprobity web site:



Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures


On Jan 29, 2007, at 2:54 PM, Angel Herraez wrote:

I am opening two new threads for Paul questions in his last post to "
loading jmol file from open babel"

On 29 Jan 2007 at 10:44, H. Paul Benton wrote:
 To all the other uses I have one more question to ask 
"If a file was loaded with no Hydrogens how can I get 
Jmol to put them on?".

Jmol cannot add hydrogens right now. Remebre it is a viewer, not a molecule builder.
I can recommend two programs that allow you to do so. One is Discovery Studio Visualizer, 
from Accelrys (formerly known by several names such as WebLab Viewer, Accelrys Viewer, 
DS Viewer, etc.)
The other is ChemSketch, from ACDLabs. This is actually a 2D chemical drawing package, 
but imports and exports MOL files and has a 3D module. 

If you haven't used any of them, go for DS Visualizer. It will open your pdb, mol, xyz etc files, 
then go to menu Tools > Hydrgens > Add and save again.

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