[Chimera-users] could not find binaries for addh and addcharge programs

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 15 08:44:42 PDT 2019

Hi Zafer Aydin,
The commands are “findhbond” (or “hbonds”) and “addcharge” — they are in the Chimera executable, and they are not separate binaries. 

For example, open your structure(s) and then use commands:

findhbond reveal true

Of course, there are other command options, and you would need to read the manual pages linked above to decide whether you want to use any of them.

If you want to use Chimera without any graphical interface (not even the Chimera window), you need to start it with the nogui option and input your structures and commands in a script.  See

 I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 15, 2019, at 7:31 AM, Zafer AYDIN <zafer.aydin at agu.edu.tr> wrote:
> Hi,
> I installed chimera software to my Ubuntu workstation. I want to add hydrogen bonds and charges to ligand molecules. I could not find the addh and addcharge executables under the chimera directory.
> I would readlly appreciate if you can provide me basic guidelines for how to add hydrogen bonds and charges to ligand molecules using chimera from command-line (not from GUI).
> Many thanks,
> Zafer Aydin
> AGÜ Computer Engineering Department
> Kayseri, Turkey

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