<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Atila,<div>Of course the hydrogen bonds are always to the hydrogen atom -- the difference is only how the lines are drawn. Many structures do not include the hydrogens, so it makes sense to draw the line from the donor heavy atom to the acceptor heavy atom. However, we recently made a change that if your structure does include hydrogens, the lines will be drawn to the hydrogens instead.</div><div><br></div><div>This is only in the newest versions, not the 1.4.1 production release. You would need to get a "daily build" download, Chimera version 1.5, to see this change.</div><div><br></div><div>I hope this helps,</div><div>Elaine<br><div>
<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><div>----------</div><div>Elaine C. Meng, Ph.D. </div><div>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</div><div>Department of Pharmaceutical Chemistry</div><div>University of California, San Francisco</div><div><br></div></div></span></div><div><div>On Sep 27, 2010, at 7:32 AM, atila petrosian wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><p class="MsoNormal" style="MARGIN: 0in 0in 10pt"><font face="times new roman,serif" size="3">Hi chimera users</font></p><p class="MsoNormal" style="MARGIN: 0in 0in 10pt"><font face="times new roman,serif" size="3">I used (find Hydrogen bonds) option for my pdb file (containing 2 strands of amino acids), but chimera show HBs that being between O and N atoms, while I want to chimera show HBs that being between O and H atoms (usually, in proteins, HB is formed between O atom of C=O group and H atom of N-H group, consequently; C=O…H-N).</font></p><p class="MsoNormal" style="MARGIN: 0in 0in 10pt"><font face="times new roman,serif" size="3">Please guide me.</font></p></blockquote></div></div></body></html>