<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div><blockquote type="cite" class=""><div class="">On Jan 31, 2017, at 12:00 AM, Kenward Vaughan <<a href="mailto:kay_jay@earthlink.net" class="">kay_jay@earthlink.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">On 01/29/2017 02:16 PM, Elaine Meng wrote:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">No problem, I actually had to think about this… there's not yet a ChimeraX command to create pseudobonds, but you can list pairs of atoms in a text file, name it something.pb and then open the file. Maybe that is still too inconvenient, however.<br class=""><br class="">For example, in ChimeraX "open 1bna" and then the attached text file (if name ends in .pb). Actually mmCIF of nucleic acids already have the base-pairing H-bonds, as you can see before opening the pb file. You can control number of dashes with ChimeraX command “style” and color using “color” with “target p” … I don’t think there’s a command for pseudobond thickness yet, however.<br class=""><br class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/style.html" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/style.html</a>><br class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class=""><br class=""></blockquote><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">It certainly gives me things to gnaw on... :-)</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">If a scene with H-bonds is generated in Chimera, can that be saved/exported with those bonds recorded in a way that ChimeraX will read them?</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Kenward</span></div></blockquote></div><br class=""><div class="">Hi Kenward,</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Strictly speaking, the answer is no. Atom specs in Chimera and ChimeraX differ. For instance, the Chimera atom spec “:11.A@ND1” in Chimera X would be “/A:11@ND1”. As you generate H-bonds in Chimera, there’s an option to save them to a file. You would then have to edit that file and swizzle things around to get the info into the atom-pair format that ChimeraX can read as pseudobonds.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline"></div><br class=""><div><blockquote type="cite" class=""></blockquote></div></div></body></html>