<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Mahendra,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Your coordinates are two-dimensional, not three-dimensional. Chimera is not going to be able to correctly determine the atom types for a two-dimensional compound, nor appropriately protonate it, nor properly minimize it. You <i>could</i> directly write a two-dimensional mol2 file from the sdf simply by dropping the runCommand("minimize") step of the processing script, but many of the mol2 atom types would be wrong.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I think you need to use some other tool for your conversion. Maybe <a href="http://openbabel.org/wiki/Main_Page">Open Babel</a>?</div><div><br></div><div>--Eric</div><div><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br><br><div><div>On Apr 29, 2015, at 11:01 AM, Mahendra B Thapa <thapamb@mail.uc.edu> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div><div><div><div><div>Dear Chimera users,<br><br></div>I am trying to convert sdf file ( downloaded from<u> diversity set</u> data from '<a href="http://scs.illinois.edu/htsf/compound_collection/nci.php">http://scs.illinois.edu/htsf/compound_collection/nci.php</a>') into mol2 format. When I ran the command chimera --nogui processSDF.py<br></div>as given the previous posting ( <a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004974.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004974.html</a>), I got the following error messages:<br>Cannot find consistent set of bond orders for ring system containing atom #0.73:1@N1<br>---<br>Unknown redo atom type: N3<br>Traceback (most recent call last):<br><br></div>Any suggestions for correcting these errors will be a good help for me.<br><br></div>Thank you,<br></div>Mahendra Thapa<br></div>University of Cincinnati,OH<br></div>
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