[chimerax-users] Adding H atoms

[Elaine Meng]

Hello Daniel,
No idea why Houdini (a program I have never used) would or would not show atoms .  We haven't had problems with saved PDB files after adding hydrogens, and ChimeraX PDB saving is careful about using the correct format.  If you are saving using the dialog opened from the menu with File... Save, just make sure you specified the correct file type to save (PDB) and did NOT turn on any options to save the displayed or selected atoms only.  As you might expect, those options would only save the atoms that are displayed or selected instead of all atoms.
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 25, 2022, at 4:47 PM, Daniel VillanuevaAvalos via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello, 
> I am adding hydrogen atoms by entering addh#1 to the command line, and it works but when I export the pdb and import it into houdini, things are messed up. Sometimes it just doesn't show up and other times, just part of the structure shows up. Am I missing something?
> 
> Thank you, 
> Daniel.