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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> $B<~@9J!(B <zhousf@szbl.ac.cn><br>
<b>Sent:</b> Tuesday, November 19, 2019 1:33 AM<br>
<b>To:</b> chimera <chimera@cgl.ucsf.edu><br>
<b>Subject:</b> To add hydrogen atoms for a dataset</font>
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<div style="clear:both"><span style="font-size:18.0px">Hi all,</span></div>
<div style="clear:both"><br>
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<div style="clear:both"><span style="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>
</span></div>
<div style="clear:both"><span style="font-size:18.0px"> So I want to add hydrogen atoms for all these compounds by Chimera.<br>
</span></div>
<div style="clear:both"><span style="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>
</span></div>
<div style="clear:both"><span style="font-size:18.0px"><br>
</span></div>
<div style="clear:both"><span style="font-size:18.0px"> My question is:<br>
</span></div>
<div style="clear:both"><span style="font-size:18.0px"> How can I avoid this problem while I want to handle numerous molecules with Chimera?<br>
</span></div>
<div style="clear:both"><span style="font-size:18.0px"> If there is a way to run Chimera in a real terminal without run Chimera in graphic interface? Or<br>
</span></div>
<div style="clear:both"><span style="font-size:18.0px"> Which bin file in Chimera_HOME can add hydrogen atoms for a molecule?<br>
</span></div>
<div style="clear:both"><span style="font-size:18.0px"><br>
</span></div>
<div style="clear:both"><span style="font-size:18.0px">Sincerely look forward to your reply.<br>
</span></div>
<div style="clear:both"><span style="font-size:18.0px">Thanks</span></div>
<div style="clear:both"><br>
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<div style="clear:both"><span style="font-size:18.0px">Best</span></div>
<div style="clear:both"><span style="font-size:18.0px">Shengfu Zhou</span></div>
<div style="clear:both"><span style="font-size:18.0px">2019.11.19<br>
</span></div>
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