<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Elaine<div><br></div><div>I'm using the <open smiles> command as per your instructions (see your message below). </div><div><br></div><div>The ligand I'm trying to build is: <b>(10E,12Z)-tetradeca-10,12-dien-1-o</b>l. The SMILES formula I'm using is: <b>C\C=C/C=C/CCCCCCCCCO</b></div><div><br></div><div>What I get is nonanol. The program returns</div><div><br></div><div><b>opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues</b></div><div><br></div><div>Obviously, I'm using a different SMILES convention than Chimera.</div><div><br></div><div>I'd appreciate you suggestion regarding the SMILES convention, I should be using.</div><div><br></div><div>All the best</div><div><br></div><div>George</div><div><br></div><div>George T. Tzotzos, PhD</div><div>Dept. of Molecular Genetics</div><div>Univ. of Gent, Belgium</div><div><br></div><div><br><div><div>On Sep 3, 2009, at 7:46 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Miriam,<br>Are you on a Mac? I'm using a Mac and was able to copy text from <br>Terminal and paste it into both those places. The copy/paste <br>procedure depends on your platform. Using the Mac aqua version, I <br>highlighted text in Terminal and pressed command-c to copy, then to <br>paste, I clicked into the blank dialog text area and pressed command- <br>v. Using the Mac X11 version, I used the same copying procedure but <br>then to paste, clicked into the blank dialog text area and then <br>clicked middle mouse button. On Windows, copy and paste may be Ctrl-c <br>and Ctrl-v.<br><br>You can also get SMILES->3D from the Chimera command line, e.g.<br><br>open smiles:C1CCC(O)CC1<br><br>and the copy/paste procedure there is the same, but again platform- <br>dependent.<br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D.<br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br>On Sep 1, 2009, at 3:09 PM, Miriam Gochin wrote:<br><br><blockquote type="cite">I have downloaded the latest build (Aug 30, 2009) and don't seem to <br></blockquote><blockquote type="cite">be able to input a SMILES string. I have tried both the Utilities - <br></blockquote><blockquote type="cite"><blockquote type="cite">Structure Diagram and the Structure Editing -> Build Structure <br></blockquote></blockquote><blockquote type="cite">tool, and in both cases I can see a box to input the SMILES string, <br></blockquote><blockquote type="cite">but the copy and paste mechanism won't work. I can enter text in <br></blockquote><blockquote type="cite">the box, but cannot paste it in, which I need to do. Thanks for <br></blockquote><blockquote type="cite">your help.<br></blockquote><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>