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<div style="font-size: 13.3333px; font-family: tahoma; color: rgb(0, 0, 0); font-weight: 400; font-style: normal;">Dear Elaine,</div>
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<div style="font-size: 13.3333px; font-family: tahoma; color: rgb(0, 0, 0); font-weight: 400; font-style: normal;">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.</div>
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<div style="font-size: 13.3333px; font-family: tahoma; color: rgb(0, 0, 0); font-weight: 400; font-style: normal;">Thanks,</div>
<div style="font-size: 13.3333px; font-family: tahoma; color: rgb(0, 0, 0); font-weight: 400; font-style: normal;">Zafer</div>
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<blockquote class="as91pFk8AX8sDPOUp66RUy8IoCRjefxNG8oLk8fg" style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">From: "Elaine Meng (meng@cgl.ucsf.edu)" <meng@cgl.ucsf.edu><br />
To: Zafer AYDIN <zafer.aydin@agu.edu.tr><br />
Cc: chimera-users@cgl.ucsf.edu<br />
Date: Fri, 15 Mar 2019 08:44:42 -0700<br />
Subject: Re: [Chimera-users] could not find binaries for addh and addcharge programs<br />
<div style="font-family: monospace, courier new, courier">Hi Zafer Aydin,<br />
The commands are “findhbond” (or “hbonds”) and “addcharge” — they are in the Chimera executable, and they are not separate binaries.<br />
<br />
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html</a>><br />
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html</a>><br />
<br />
For example, open your structure(s) and then use commands:<br />
<br />
findhbond reveal true<br />
addcharge<br />
<br />
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.<br />
<br />
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<br />
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html</a>><br />
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html</a>><br />
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a>><br />
<br />
I hope this helps,<br />
Elaine<br />
-----<br />
Elaine C. Meng, Ph.D. <br />
UCSF Chimera(X) team<br />
Department of Pharmaceutical Chemistry<br />
University of California, San Francisco<br />
<br />
> On Mar 15, 2019, at 7:31 AM, Zafer AYDIN <<a href="mailto:zafer.aydin%40agu.edu.tr">zafer.aydin@agu.edu.tr</a>> wrote:<br />
><br />
> Hi,<br />
> <br />
> 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.<br />
> <br />
> 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).<br />
> <br />
> Many thanks,<br />
> <br />
> Zafer Aydin<br />
> AGÜ Computer Engineering Department<br />
> Kayseri, Turkey<br />
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