<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 Kersey,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I assume you mean the MD Movie tool. AFAIK, PDB format doesn’t support differing connectivity for different members of a multi-MODEL PDB file. I’m not sure which model Chimera uses the CONECT records from, but it’s either the first or last, and that is then applied to all the models. The result in MD Movie is one model, with one set of atoms and bonds, with the atoms repositioned every frame.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>If your CONECT records are merely indicating reasonable chemical bonding, there is a hidden feature of MD Movie to force it to recompute the bonds based on reasonable bonding distances every frame. If you run the attached script after starting MD Movie (simply by opening it with File->Open), it will turn on the recomputation mode. The recomputation won’t start until you start playing the trajectory, so the initial frame may look wrong until you start playing.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); 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; 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></div></div></body></html>