<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Charles,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Alternatively, you can also do this with the graphical interface. Just add each conformation twice when you are adding conformations. Then, choose the second conformation in the final list you've made (i.e. the second copy of your first conformation) and change "interpolation steps" to 15 (for a half-second pause). Then choose the third state and change the interpolation steps to however many you want when it's moving. Then choose the fourth state and use 15 again, etc.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I notice that the final list of conformations wants you to click in with the mouse to change which one you're working on -- the up/down arrows keys seem to change the conformation chosen but don't update the rest of the interface, so beware of that.</div><div><br></div><div>--Eric</div><div> <br><span class="Apple-style-span" style="font-size: 16px; "> Eric Pettersen</span><br><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; "> 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><div><div><br></div><div>On May 4, 2011, at 12:57 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Sigh, the coordset commands in my previous reply are not quite right, you would put the model number before the frames. Sorry about that. However, the commands are all correct within the "trmovie" example command file discussed in that message. <br>Elaine<br><br>On May 4, 2011, at 12:51 PM, Elaine Meng wrote:<br><br><blockquote type="cite">Hi Charles,<br></blockquote><blockquote type="cite">It can be done with commands. First you would create the morph trajectory, then use a Chimera command script (just open a plain text file containing the commands) of the general form:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">movie record [options]<br></blockquote><blockquote type="cite">coordset 1,20 #3; wait 20<br></blockquote><blockquote type="cite">wait 10<br></blockquote><blockquote type="cite">coordset 21,40 #3; wait 20<br></blockquote><blockquote type="cite">wait 10<br></blockquote><blockquote type="cite">coordset 41,60 #3; wait 20<br></blockquote><blockquote type="cite">movie stop<br></blockquote><blockquote type="cite">movie encode [options]<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">where [options] is not meant literally but would give your desired movie settings, and you would also change other things depending on which model is your trajectory and which frames cover the transitions, and how long you would like the pauses to be. I would also recommend saving the session with your morph trajectory in the desired orientation so you can revisit it later and easily re-make the movie with any needed variations.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">There is an example command file showing a similar procedure...<br></blockquote><blockquote type="cite">the "trmovie" example includes morphing and uses coordset to play parts of the trajectory and does other stuff between the uses of coordset (it actually does the morph creation too, but it may be easier for you to do that part beforehand):<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">... and the resulting movie is in the Animation Gallery, currently third on this page:<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/animations/animations.html">http://www.cgl.ucsf.edu/chimera/animations/animations.html</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">More info on movies and movie-related commands:<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html</a>><br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I hope this helps,<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite">-----<br></blockquote><blockquote type="cite">Elaine C. Meng, Ph.D. <br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></blockquote><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote><blockquote type="cite">University of California, San Francisco<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On May 4, 2011, at 11:51 AM, Charles Greenberg wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">I have a 3-state structure and I'm currently using morph conformations <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">to interpolate between them. This works very nicely, but I'd like the <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">output movie to pause for half a second (a few frames) during each of <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the three key states. Anyone know how to do this? I know you can add <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">behaviors during particular frames, but I don't know how to make it <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">pause. Thanks!<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">--Charles<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Chimera-users mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></blockquote><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><span class="Apple-style-span" style="font-size: medium;"><br></span><br class="Apple-interchange-newline"></div></span> </div><br></body></html>