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

[Elaine Meng]

Please see the last paragraph of my previous reply.

First to figure out the commands you want, you would have to try them yourself in the GUI.  Then, you would put the commands in a script.  Then you would start Chimera with the nogui option and input your script.  These topics are covered in the links I sent.

Best,
Elaine

> On Mar 15, 2019, at 9:11 AM, Zafer AYDIN <zafer.aydin at agu.edu.tr> wrote:
> 
> 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/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/options.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> 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
>