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

[Zafer AYDIN]

Dear Elaine,

I want to be able to run these commands (findhbond and addcharge) from Linux 
command-line only. I don't know how I can do it through the chimera 
executable. Can you send me an example command-line that does that? I don't 
want to open structures in GUI.

Thanks,
Zafer

From: "Elaine Meng (meng at cgl.ucsf.edu)" <meng at cgl.ucsf.edu>
To: Zafer AYDIN <zafer.aydin at agu.edu.tr>
Cc: chimera-users at cgl.ucsf.edu
Date: Fri, 15 Mar 2019 08:44:42 -0700
Subject: Re: [Chimera-users] could not find binaries for addh and addcharge 
programs


Hi Zafer Aydin,
The commands are “findhbond” (or “hbonds”) and “addcharge” — 
they are in the Chimera executable, and they are not separate binaries.
 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html 
[http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html]>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html 
[http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html]>

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

findhbond reveal true
addcharge

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
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html 
[http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html]>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html 
[http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html]>
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html 
[http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html]>

 I hope this helps,
Elaine
-----
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 
[mailto:zafer.aydin%40agu.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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