<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jan 28, 2009, at 7:22 AM, Katherine Parra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello!<br>I'm trying to get the hydrogen bonds between some selected residues during a trajectory, using per frame commands from tools. But when I get the possible hydrogen bonds formed between the selected residues I also get the following error message in the Reply Log:<br> <i>Skipping possible acceptor with bad geometry: #0:2108@O<br>Wrong number of grandchild atoms for phi/psi acceptor #0:2108@O<br></i>What could be happening?</blockquote><br></div><div>Hi Katherine,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>A more verbose version of the error message might be: atom #0:2108@O has been classified as a phi/psi acceptor as per Mills <i>et al</i> (full cite in FindHBond docs) but the number of atoms bonded to #0:2108@O's neighbor atoms ("grandchild atoms") is in conflict with that classification.<br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>The most likely cause is that #0:2108@O's bonds are wrong or that its neighbor atoms' bonds are wrong. There is also some chance that Chimera has computed the wrong atom type for #0:2108@O or its neighbors. If you were working with a single structure instead of a trajectory then it might also be possible that :2108 is a standard residue with missing atoms (Chimera assigns standard residue atom types using templates instead of computing them) but trajectories typically don't have missing atoms.<br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>To investigate, you should have a look at #0:2108@O's atom type and it and its neighbor's bonds. To see the atom type open the command lines (Favorites->Command Line) and type "sel #0:2108@o" and then use Actions->Label->IDTAM type. To see what the atom type means, look at this table: <a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html">Atom Types in Chimera</a> . If the atom type seems wrong, you can change it using the "setattr" command (<i>e.g.</i> to change it to O3, type: "setattr a idatmType O3 #0:2108@o"). If the atom type seems okay, look at the bonds and particularly the neighbor's bonds. If there are extra or missing bonds you can fix that using the bond/~bond command (type "help bond" in the command line for info).</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>You could send me the trajectory to look at if you feel think the problem is wrong atom typing or Chimera getting the bonding information wrong, and I would try to fix it.<br></div><div><br></div><div>--Eric</div><br><br><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; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br></body></html>