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Hi Tyler,<div><span class="Apple-tab-span" style="white-space:pre"> </span>The problem is that Chimera "knows" the atom types of standard residues and doesn't try to compute them from scratch. Therefore it assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the find-hbond computation as it looks for the planarity of the ND1 and sees it bonded to nothing!</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>For what you want to do, you want to get that atom's residue changed. Do this:</div><div><br></div><div>1) Control-double click on the ND1 atom</div><div>2) Chose "Modify Atom" from the resulting popup menu.</div><div>3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral"</div><div>4) Change "Bonds" to 3</div><div>5) In the "Residue Name" section, use the "new residue" option with "NH3" as the name and chain "het"</div><div>5) Click the Change button</div><div><br></div><div>That should give you what you want.</div><div><br></div><div>--Eric</div><div><br><div> <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; "><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></span></div><br><div><div>On May 22, 2008, at 10:25 AM, Tyler Arbour wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Wow, I didn't expect a response for this...great! I was actually just trying to create a figure representing a computational model that I am using. Starting from the crystal structure, I wanted to actually change the histidinal N to a simple NH3 molecule. I am just trying to get familiar with Chimera--I usually use DS Viewerpro for modifying structures, and it doesn't seem like Chimera is well-suited to this type of modification. If you have any advice on an easy way to make this conversion so that I have a nice figure, I'd greatly appreciate it! Thanks.<div><br></div><div>Tyler</div><div><br><div><div>On May 22, 2008, at 11:17 AM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Tyler,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Your structure seems to have a histidine residue (residue 159 in chain A) that consists solely of an ND1 atom! How did you manage that?<br></div><div><br></div><div>--Eric</div><br><br><div> <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="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><br class="Apple-interchange-newline"></span> </div><br></div></blockquote></div><br></div></blockquote></div><br></div></body></html>