<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Feb 6, 2010, at 6:25 AM, Keith Battle wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-US" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">Hello Chimera team,<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; ">I recently conducted a MD simulation of a 12-mer peptide adjacent to a hydroxyapatite crystal using NAMD 2.6. When I viewed the output coordinates from the simulation in pdb format using Chimera 1.4, the protein ribbon was broken and the hydrogens of certain residues were not bonded but in close proximity. All of the non-bonded hydrogens were colored purple by default. The waters of the system and the crystal looked normal. Overall, the protein looked distorted. I decided to visualize the peptide using VMD 1.8.7 and to my surprise the protein ribbon was intact with all hydrogens bonded to their respective residues. Any insight into why this difference occurred would be greatly appreciated.</div></div></div></span></blockquote><br></div><div>Hi Keith,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Assuming we're talking about the PDB file you attached to Trac ticket #8165, then I guess I'm puzzled. Chimera 1.4 displays it correctly AFAICT. Certainly all the hydrogens are bonded. I've attached two images of the peptide, one without ribbons and one with. Some of the side chains of the one with ribbons look a little weird because the carbon alpha position is interpolated to lie on the ribbon which can produce a weird looking CA-CB bond (and N-CD bond in the case of proline).</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Now, the PDB file does have problems. NAMD has put a lot of garbage in the 'element' column of the ATOM/HETATM records (last column on the right). All the calciums in your crystal have element 'C' instead of 'CA' and some (but not all) of the hydrogens in your protein are 'LP' (lone pair) instead of 'H'. Chimera honors the former unfortunately but knows that the latter is garbage and falls back to guessing the element from the atom name and correctly deduces that it's hydrogen.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>From your description it sounds like that -- for you -- Chimera is in fact getting the element type wrong for those hydrogens and possibly other atoms as well. Are you really opening precisely the file you attached in the 1.4 version of Chimera? If you're certain that that's the case, try labeling the disconnected atoms with their element types (Actions->Label->element) and let me know what they are.</div><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></div></span></div><br><div></div></div><div><img height="735" width="747" apple-width="yes" apple-height="yes" src="cid:395F975E-76AE-4A1F-B2B5-C9F156AE5953@cgl.ucsf.edu"><img height="735" width="747" apple-width="yes" apple-height="yes" src="cid:C503A020-E0A5-4B56-94CB-21FC5FB27937@cgl.ucsf.edu"></div></body></html>