<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="">Hi Shengfu,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </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" style="white-space:pre"> </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 href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html" class="">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" style="white-space:pre"> </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 style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div></div><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 20, 2019, at 8:56 AM, Williams, Joanne <<a href="mailto:Joanne.Williams@ucsf.edu" class="">Joanne.Williams@ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class="Apple-interchange-newline"><br class=""></div><div id="Signature" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div class=""></div><div class=""></div><div class=""></div><div class=""></div><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><blockquote type="cite" style="font-family: "Times New Roman"; font-size: 16px;" class=""><div class="WordSection1"><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-family: "helvetica neue", helvetica, arial, sans-serif; font-size: 11.55pt; color: rgb(53, 58, 63); background-color: rgb(255, 255, 255);" class=""></span></p><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><a class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">-- </span></a></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">JoAnne Williams | Executive Analyst to:</span></span></div><p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class=""> </span></span></p><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Matt Jacobson, Professor and Department Chair</span></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Pam England, Professor</span></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Zev Gartner, Professor</span></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Tom Ferrin, Professor</span></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Department of Pharmaceutical Chemistry</span></b></span></div><p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class=""> </span></span></p><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Wallace Marshall, Professor</span></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Center for Cellular Construction | Department of Biochemistry & Biophysics</span></b></span></div><p style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class=""> </span></span></p><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">600 16th Street, Room N372 | UCSF MC2200 | San Francisco, CA 94158 </span></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; background-color: white;" class=""><span class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Phone: (415) 418-3079 | Email: <a href="mailto:joanne.williams@ucsf.edu" class="">joanne.williams@ucsf.edu</a></span></span></div><p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span style="font-family: "helvetica neue", helvetica, arial, sans-serif; font-size: 11.55pt; color: rgb(53, 58, 63); background-color: rgb(255, 255, 255);" class=""></span></p></div></blockquote></div></div></div><div class=""><div id="appendonsend" class=""></div><hr tabindex="-1" style="display: inline-block; width: 505.671875px;" class=""><div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>周盛福 <<a href="mailto:zhousf@szbl.ac.cn" class="">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 href="mailto:chimera@cgl.ucsf.edu" class="">chimera@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>To add hydrogen atoms for a dataset</font><div class=""> </div></div><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: 18px;" class="">Hi all,</span></div><div style="clear: both;" class=""><br class=""></div><div style="clear: both;" class=""><span style="font-size: 18px;" class=""> 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 style="clear: both;" class=""><span style="font-size: 18px;" class=""> So I want to add hydrogen atoms for all these compounds by Chimera.<br class=""></span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class=""> 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 style="clear: both;" class=""><span style="font-size: 18px;" class=""><br class=""></span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class=""> My question is:<br class=""></span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class=""> How can I avoid this problem while I want to handle numerous molecules with Chimera?<br class=""></span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class=""> If there is a way to run Chimera in a real terminal without run Chimera in graphic interface? Or<br class=""></span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class=""> Which bin file in Chimera_HOME can add hydrogen atoms for a molecule?<br class=""></span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class=""><br class=""></span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class="">Sincerely look forward to your reply.<br class=""></span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class="">Thanks</span></div><div style="clear: both;" class=""><br class=""></div><div style="clear: both;" class=""><span style="font-size: 18px;" class="">Best</span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class="">Shengfu Zhou</span></div><div style="clear: both;" class=""><span style="font-size: 18px;" class="">2019.11.19<br class=""></span></div></div></div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>