<div class="__aliyun_email_body_block"><div  style="line-height:1.7;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><div  style="clear:both;"><span  style="font-size:16.0px;">Hi Eric,</span></div><div  style="clear:both;"><br ></div><div  style="clear:both;"><span  style="font-size:16.0px;">    Thanks for your advice.</span></div><div  style="clear:both;"><span  style="font-size:16.0px;">    I have tried to run chimera with --nogui option, then I can run almost all commands smoothly.  Thank you for your contribution to share us a perfect package.<br ></span></div><div  style="clear:both;"><span  style="font-size:16.0px;"><br ></span></div><div  style="clear:both;"><span  style="font-size:16.0px;">Best,<br ></span></div><div  style="clear:both;"><span  style="font-size:16.0px;">Shengfu Zhou,<br ></span></div><div  style="clear:both;"><span  style="font-size:16.0px;">2019.11.21</span><span  class="tlid-translation translation" lang="en"><br ></span></div><div  style="clear:both;"><br ></div><div  style="clear:both;"><br ></div><blockquote  style="margin-right:.0px;margin-top:.0px;margin-bottom:.0px;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><div  style="clear:both;">------------------------------------------------------------------</div><div  style="clear:both;">发件人：Eric Pettersen <pett@cgl.ucsf.edu></div><div  style="clear:both;">发送时间：2019年11月21日(星期四) 07:19</div><div  style="clear:both;">收件人：周盛福 <zhousf@szbl.ac.cn></div><div  style="clear:both;">抄　送：Chimera User Help <chimera-users@cgl.ucsf.edu></div><div  style="clear:both;">主　题：Re: [Chimera-users] Fw: To add hydrogen atoms for a dataset</div><div  style="clear:both;"><br ></div>Hi Shengfu,<div  class=""><span  class="Apple-tab-span"> </span>Glad to hear that Chimera does a good job of hydrogen addition relative to other packages.  It can still get things wrong with extremely complex ring systems or poor starting coordinates, but seems pretty reliable otherwise.  I’m glad you like it!</div><div  class=""><span  class="Apple-tab-span">       </span>One problem here is that Python memory consumption may not go down when in the middle of script execution.  You can in fact run Chimera from a terminal with no graphical interface by giving the --nogui option, as described here: <a  class="" href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html" target="_blank">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html</a> .  Therefore you could break your computation into batches of 500 or 1000 molecules and possibly work around the memory problem that way.</div><div  class=""><span  class="Apple-tab-span">  </span>There is no standalone binary for adding hydrogens within Chimera.  There is a Python module (AddH), but it relies heavily on Chimera’s built-in atom typing, and which is therefore difficult to run outside the context of Chimera.</div><div  class=""><br  class=""></div><div >—Eric</div><div  class=""><div  class=""><div  class="" style="caret-color:#000000;font-variant-caps:normal;text-align:start;text-indent:.0px;"><span  class="Apple-tab-span" style="color:#000000;font-family:Helvetica;font-size:12.0px;font-style:normal;font-weight:400;text-transform:none;"><br  class="Apple-interchange-newline"> Eric Pettersen</span></div><div  class="" style="caret-color:#000000;font-variant-caps:normal;text-align:start;text-indent:.0px;"><span  style="color:#000000;font-family:Helvetica;font-size:12.0px;font-style:normal;font-weight:400;text-transform:none;">UCSF Computer Graphics Lab</span></div><div  class="" style="caret-color:#000000;font-variant-caps:normal;text-align:start;text-indent:.0px;"><span  style="color:#000000;font-family:Helvetica;font-size:12.0px;font-style:normal;font-weight:400;text-transform:none;"><br  class=""></span></div></div><div ><br  class=""><div  class="">On Nov 20, 2019, at 8:56 AM, Williams, Joanne <<a  class="" href="mailto:Joanne.Williams@ucsf.edu" target="_blank">Joanne.Williams@ucsf.edu</a>> wrote:</div><br  class="Apple-interchange-newline"><div  class=""><div  class="" style="font-variant-caps:normal;text-align:start;text-indent:.0px;"><span  style="font-style:normal;font-weight:400;text-transform:none;"><br  class="Apple-interchange-newline"><br  class=""></span></div><div  class="" id="Signature" style="caret-color:#000000;font-variant-caps:normal;text-align:start;text-indent:.0px;"><div  class="WordSection1"><div  class="" style="margin:.0in .0in .0px;"><a  class="" href="#this" style="font-style:normal;font-weight:400;text-transform:none;font-size:16.0px;font-family:Times New Roman,serif;"><span  class="" style="font-size:13.0px;font-family:Calibri,sans-serif;">-- </span></a></div><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;">JoAnne Williams | Executive Analyst to:</span></div><p  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;"> </span></p><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;">Matt Jacobson, Professor and Department Chair</span></div><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;">Pam England, Professor</span></div><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;">Zev Gartner, Professor</span></div><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;">Tom Ferrin, Professor</span></div><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;text-transform:none;font-weight:bold;font-size:13.0px;font-family:Calibri,sans-serif;">Department of Pharmaceutical Chemistry</span></div><p  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;"> </span></p><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;">Wallace Marshall, Professor</span></div><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;text-transform:none;font-weight:bold;font-size:13.0px;font-family:Calibri,sans-serif;">Center for Cellular Construction | Department of Biochemistry & Biophysics</span></div><p  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;"> </span></p><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;">600 16th Street, Room N372 | UCSF MC2200 | San Francisco, CA 94158 </span></div><div  class="" style="margin:.0in .0in .0px;background-color:white;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-size:13.0px;font-family:Calibri,sans-serif;">Phone: (415) 418-3079 | Email: <a  class="" href="mailto:joanne.williams@ucsf.edu" target="_blank">joanne.williams@ucsf.edu</a></span></div></div><div  class=""><hr  class="" style="font-family:Helvetica;font-size:12.0px;font-style:normal;font-weight:400;text-transform:none;display:inline-block;width:505.7px;"><div  class="" id="divRplyFwdMsg"><span  style="font-style:normal;font-weight:400;text-transform:none;font-size:15.0px;font-family:Calibri,sans-serif;"><b  class="">From:</b><span  class="Apple-converted-space"> </span>周盛福 <<a  class="" href="mailto:zhousf@szbl.ac.cn" target="_blank">zhousf@szbl.ac.cn</a>><br  class=""><b  class="">Sent:</b><span  class="Apple-converted-space"> </span>Tuesday, November 19, 2019 1:33 AM<br  class=""><b  class="">To:</b><span  class="Apple-converted-space"> </span>chimera <<a  class="" href="mailto:chimera@cgl.ucsf.edu" target="_blank">chimera@cgl.ucsf.edu</a>><br  class=""><b  class="">Subject:</b><span  class="Apple-converted-space"> </span>To add hydrogen atoms for a dataset</span><div  class=""><span  style="font-family:Helvetica;font-size:12.0px;font-style:normal;font-weight:400;text-transform:none;"> </span></div></div><div  class="" style="line-height:1.7;"><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">Hi all,</span></div><div  class="" style="clear:both;"><span  style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;"><br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">    I have used UCSF Chimera for several years and find that Chimera has a perfect behavior in adding hydrogen atoms for small molecules. It is easier to add wrong hydrogen atoms onto nitrogen heterocycles groups with other software, including openbabel, MGLTools, PyMol, etc. Now I want to add hydrogen atoms for a dataset, which contains more than 10 thousands ligands for virtual screening. And a great number of compounds in this dataset have nitrogen heterocycle groups.<br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">    So I want to add hydrogen atoms for all these compounds by Chimera.<br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">    When I try to run a script in Favorites > Command line by read a MOL, addh and delete the MOL in cycle. I found that the memory usage of Chimera keep growing although I have delete the previous MOLs.<br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;"><br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">    My question is:<br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">        How can I avoid this problem while I want to handle numerous molecules with Chimera?<br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">        If there is a way to run Chimera in a real terminal without run Chimera in graphic interface?  Or<br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">        Which bin file in Chimera_HOME can add hydrogen atoms for a molecule?<br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;"><br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">Sincerely look forward to your reply.<br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">Thanks</span></div><div  class="" style="clear:both;"><span  style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;"><br  class=""></span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">Best</span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">Shengfu Zhou</span></div><div  class="" style="clear:both;"><span  class="" style="font-style:normal;font-weight:400;text-transform:none;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:18.0px;">2019.11.19<br  class=""></span></div></div></div></div><span  class="" style="caret-color:#000000;font-family:Helvetica;font-size:12.0px;font-style:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;">_______________________________________________</span><br  class="" style="caret-color:#000000;font-family:Helvetica;font-size:12.0px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:.0px;text-transform:none;white-space:normal;word-spacing:.0px;"><span  class="" style="caret-color:#000000;font-family:Helvetica;font-size:12.0px;font-style:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;">Chimera-users mailing list:<span  class="Apple-converted-space"> </span></span><a  class="" href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" style="font-family:Helvetica;font-size:12.0px;font-style:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;">Chimera-users@cgl.ucsf.edu</a><br  class="" style="caret-color:#000000;font-family:Helvetica;font-size:12.0px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:.0px;text-transform:none;white-space:normal;word-spacing:.0px;"><span  class="" style="caret-color:#000000;font-family:Helvetica;font-size:12.0px;font-style:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;">Manage subscription:<span  class="Apple-converted-space"> </span></span><a  class="" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank" style="font-family:Helvetica;font-size:12.0px;font-style:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></div><br  class=""></div></blockquote><div  style="line-height:20.0px;clear:both;"><br ></div></div></div>