<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">From the help page for the Morph Conformations tool:<div><br></div><div><a name="ksdssp" style="color: rgb(0, 0, 0); font-family: Times; "><b>MD Movie does not automatically re-evaluate secondary structure</b>.</a><span style="font-family: Times; "> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html" target="_top" style="font-family: Times; "><b>MD Movie</b></a><span style="font-family: Times; "> does not automatically recompute secondary structure assignments as coordinates change across a trajectory. This is relevant when </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#ribbon" style="font-family: Times; ">ribbons</a><span style="font-family: Times; "> are displayed and the conformational changes are large enough to alter secondary structure assignments. To recompute secondary structure at each frame, use a </span><a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame" style="font-family: Times; ">per-frame script</a><span style="font-family: Times; "> in </span><a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html" target="_top" style="font-family: Times; "><b>MD Movie</b></a><span style="font-family: Times; "> that includes the Chimera command </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html" style="font-family: Times; "><b>ksdssp</b></a><span style="font-family: Times; ">.</span></div><div><font face="Times"><br></font></div><div>--Eric</div><div><div><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br><br></div><div><div>On Oct 26, 2013, at 3:34 PM, "Kang, Yanyong" <<a href="mailto:Yanyong.Kang@vai.org">Yanyong.Kang@vai.org</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-US" link="blue" vlink="purple" style="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: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="WordSection1" style="page: WordSection1; "><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Dear Chimera developer,<o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I have some problem for making morph movie. My start model has the secondary structure, but the final model loses most of the secondary structure. My morph movie could not show the secondary structure transition of the protein structure. If I change final model as the start model, the start model is as the final model. Secondary structure is the same with the start model. Do you have any ideas to solve this issue? Thank you very much<o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Best,<o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Yanyong<o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Dr. Yanyong Kang<o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Laboratory of Structural Sciences<o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Van Andel Research Institute<o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Tel, 616-234-5446<o:p></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline; ">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline; ">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div><br><br></body></html>