<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Ryan,<div class=""><br class=""></div><div class=""> ChimeraX has a "morph" command. Here's an example using it</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 2vaa</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 2vab</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>matchmaker #2 to #1</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>morph #1,2</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>save morph.pdb model #3 allCoordsets true</div><div class=""><br class=""></div><div class="">Morphing of course only contains the atoms that are in both structures. So if you have an unbound and a bound state, and the bound tapasin is only in one structure then it will not be included in the morph since there is nothing to morph it to in the unbound state. You can delete chains that the two structures do not have in common before morphing, or you can use the same true option to the morph command "morph #1,2 same true" which will ignore chains which do not appear in both structures.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 29, 2022, at 9:28 AM, Kissinger, Ryan (NIH/NIAID) [C] <<a href="mailto:ryan.kissinger@nih.gov" class="">ryan.kissinger@nih.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Tom,<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’m trying to create a morph animation in ChimeraX and I am having a lot of trouble finding decent tutorials online. I have pdb entries for unbound MHC1 and Tapasin and bound MHC1 and Tapasin. If possible I would like to morph between the bound and unbound forms. I would like to do this with ribbon and the atomic models. Any advice?<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best Regards,<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Ryan</div></div></div></blockquote></div><br class=""></div></body></html>