<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Actually, Morph Conformations has a bug right now in showing altlocs. You need to make two copies of your PDB and in one strip the B locations of that residue and the replace the 'A' indicator letters with blanks, and in the other do the converse. If you open those two files you should be able to morph between them as Elaine describes.<div><br></div><div>--Eric</div><div><br><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; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Aug 19, 2008, at 11:26 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Dave,<br>The Morph Conformations tool (under Tools... Structure Comparison) <br>generates interpolated intermediate structures and then opens the <br>result as a trajectory in the MD Movie tool. With MD Movie you can <br>interactively play the trajectory but also save a movie file.<br><br>These are not in command form, however. Take a look and see if these <br>tools allow you to do what you want...<br><br>Morph Conformations:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html</a> <br><blockquote type="cite"><br></blockquote><br>MD Movie:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html</a> <br><blockquote type="cite"><br></blockquote><br>Tutorials with morphing examples:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/</a> <br>squalene.html><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html</a> <br><blockquote type="cite"><br></blockquote><br>Tutorial that includes saving a movie with MD Movie:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1</a> <br><blockquote type="cite"><br></blockquote><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br><br>On Aug 19, 2008, at 11:11 AM, David Chenoweth wrote:<br><br><blockquote type="cite">Dear Chimera team,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Is there a movie command that can easily depict the interconversion<br></blockquote><blockquote type="cite">between two alternate conformations in a nucleic acid or protein<br></blockquote><blockquote type="cite">residue (designated conformation a and b) within a pdb file. I am<br></blockquote><blockquote type="cite">really trying to illustrate with a movie how the phosphates flip<br></blockquote><blockquote type="cite">between two well defined states in an ultra-high resolution DNA<br></blockquote><blockquote type="cite">crystal structure using a chimera movie.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks in advance,<br></blockquote><blockquote type="cite">Dave Chenoweth<br></blockquote><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>