<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Glad it works! Happy I could help.<div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 21, 2019, at 12:51 AM, 周盛福 <<a href="mailto:zhousf@szbl.ac.cn" class="">zhousf@szbl.ac.cn</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="__aliyun_email_body_block"><div style="line-height: 1.7; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class=""><div style="clear:both;" class=""><span style="font-size:16.0px;" class="">Hi Eric,</span></div><div style="clear:both;" class=""><br class=""></div><div style="clear:both;" class=""><span style="font-size:16.0px;" class=""> Thanks for your advice.</span></div><div style="clear:both;" class=""><span style="font-size:16.0px;" class=""> 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 class=""></span></div><div style="clear:both;" class=""><span style="font-size:16.0px;" class=""><br class=""></span></div><div style="clear:both;" class=""><span style="font-size:16.0px;" class="">Best,<br class=""></span></div><div style="clear:both;" class=""><span style="font-size:16.0px;" class="">Shengfu Zhou,<br class=""></span></div><div style="clear:both;" class=""><span style="font-size:16.0px;" class="">2019.11.21</span><span class="translation tlid-translation" lang="en"><br class=""></span></div><div style="clear:both;" class=""><br class=""></div><div style="clear:both;" class=""><br class=""></div><blockquote style="margin-right: 0px; margin-top: 0px; margin-bottom: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class=""><div style="clear:both;" class="">------------------------------------------------------------------</div><div style="clear:both;" class="">发件人：Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>></div><div style="clear:both;" class="">发送时间：2019年11月21日(星期四) 07:19</div><div style="clear:both;" class="">收件人：周盛福 <<a href="mailto:zhousf@szbl.ac.cn" class="">zhousf@szbl.ac.cn</a>></div><div style="clear:both;" class="">抄 送：Chimera User Help <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>></div><div style="clear:both;" class="">主 题：Re: [Chimera-users] Fw: To add hydrogen atoms for a dataset</div><div style="clear:both;" class=""><br class=""></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 class="">—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="font-family: Helvetica; font-size: 12px; 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="font-family: Helvetica; font-size: 12px; font-style: normal; font-weight: 400; text-transform: none;" class="">UCSF Computer Graphics Lab</span></div><div class="" style="caret-color:#000000;font-variant-caps:normal;text-align:start;text-indent:.0px;"><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-weight: 400; text-transform: none;" class=""><br class=""></span></div></div><div class=""><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;" class=""><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="x-msg://3/#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="" 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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;" class=""><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;" class=""> </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;" class=""><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;" class=""><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;" class=""><br class=""></div></div></div>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>