<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jan 31, 2010, at 3:32 PM, Nancy wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello,<br><br>I am performing protein-ligand docking simulations, and the preferred ligand input file format is Mol2. I obtained some of my ligand structures from PubChem in SDF format, and I noticed that the SDF files contain partial charges ("PUBCHEM_MMFF94_PARTIAL_CHARGES"). Is there a way to preserve the charges in Chimera when converting to Mol2 file format?</blockquote><br></div><div>Hi Nancy,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I don't know if you are going to continue to use Chimera for your SDF->Mol2 conversion given my response to your other question, but Chimera doesn't handle the PubChem-only fields, no. I wasn't aware they existed until your question! Now that I know about them I think Chimera should handle them. I will open an enhancement-request ticket in the Chimera Trac database for this feature. In the interim, you would have to extract the charge from the SDF file yourself and write a "defattr" file to get them assigned as the "charge" attribute of each atom, as outlined here:</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/defattr.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/defattr.html</a></div><div><br></div><div>I've attached an SDF and corresponding defattr file.</div><span class="Apple-tab-span" style="white-space:pre"> </span>You could even do this after generating a Mol2 via OpenBabel (and reading that into Chimera) since Chimera will honor Mol2 atom/bond types that came from the input and will leave them unchanged on output.<div><br></div><div>--Eric</div><div><br></div><div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div></span></div></div></body></html>