<div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">Thank you Elaine, your information really helped me a lot. Finally, I got the right url link for many Chimera Scripts: <a href="https://www.rbvi.ucsf.edu//trac/chimera/wiki/Scripts">https://www.rbvi.ucsf.edu//trac/chimera/wiki/Scripts</a></div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">And I have already found what I want in here: <a href="https://sourceforge.net/p/rdkit/mailman/message/36610151/">https://sourceforge.net/p/rdkit/mailman/message/36610151/</a></div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">Thanks again,</div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">Best regards,</div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif"><br></div><div class="gmail_default" style="font-family:"trebuchet ms",sans-serif">Broto Santoso</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 16 Jan 2023 at 00:12, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Broto,<br>
I can't really say anthing more than is already in the written help:<br>
<br>
First, figure out the Chimera commands that you need, such as by typing them into the command line.<br>
<br>
Second, after you figure out the Chimera commands, then this page explains how to put them into a python script and run on multiple structure files.<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a>><br>
<br>
See the Programmer's Guide for more info and example scripts:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.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 Jan 14, 2023, at 4:14 AM, Broto Santoso via Chimera-dev <<a href="mailto:chimera-dev@cgl.ucsf.edu" target="_blank">chimera-dev@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Dear Chimera Staff,<br>
> <br>
> I want to run some chimera commands (such as add hydrogen and add charge) via python script for multiple files and save them as mol2 or pdb. I have read some examples, but still know nothing. Would you like to give me more about the script, how to make it easily?<br>
> <br>
> Thank you<br>
> <br>
> Best regards,<br>
> <br>
> -- <br>
> Broto Santoso<br>
> Laboratorium Kimia Farmasi<br>
> Fakultas Farmasi UMS<br>
> mobile: +6282136414379 (no call, sms only)<br>
> My Youtube Channel<br>
<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><font face="trebuchet ms, sans-serif" color="#0000ff"><b>Broto Santoso</b></font><div><div><font face="trebuchet ms, sans-serif">Laboratorium Kimia Farmasi</font></div><div><font face="trebuchet ms, sans-serif">Fakultas Farmasi UMS</font></div><div><font face="trebuchet ms, sans-serif">mobile: +6282136414379 (<i>no call, sms only</i>)<br></font></div><div><font face="trebuchet ms, sans-serif"><a href="https://www.youtube.com/channel/UCCiJ8VZ1Vd3rVtywWkm4GyQ" target="_blank">My Youtube Channel</a><br></font></div><div><font face="trebuchet ms, sans-serif"><i>Please, do not share GDrive or attachment</i><br></font></div></div></div></div></div>