<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On May 4, 2011, at 10:05 AM, Francesco Pietra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello:<br>i had partial failure in addH to a natural product. H at a quaternary,<br>chiral C was not added in spite of repeated attempts.<br></div></blockquote><div><br></div>Hi Francesco,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>My guess is that Chimera does not believe that the problem carbon is sp3, which Chimera decides based on the carbon's bond geometry. You can see what atom type Chimera assigned to that carbon by selecting it and then doing Actions->Label->IDATM type. An sp3 carbon would be "C3". An sp2 carbon would be "C2". A full table of atom types is here:</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/idatm.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/idatm.html</a></div><div><br></div><div>You can force Chimera to believe the carbon is sp3 by selecting it and then using this command:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>setattr a idatmType C3 sel</div><div><br></div><div>It would also probably be helpful if you used Help->Report A Bug to submit a bug report on this problem, attaching the structure file.</div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><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-size: 16px; "><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-size: 16px; "><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><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div><blockquote type="cite"><div><br>All Hs were added by my favorite drawer (for organic compounds);<br>however, this changes the coordinates, which is not what I want.<br><br>I solved the issue by transferring the chimera pdb output to vmd,<br>adding the missing H with Molefacture.<br><br>On the other hand, Molefacture, if asked to add all Hs, resulted in<br>incorrect stereochemistry at -O-CH3 and some -C-CH3 (inverted<br>umbrella, which could not be reversed).<br><br>francesco pietra<br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><span class="Apple-style-span" style="font-size: medium;"><br></span><br class="Apple-interchange-newline"></div></span> </div><br></body></html>