<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><DIV>On Sep 5, 2007, at 10:37 AM, Wang, Xuelin wrote:</DIV><BLOCKQUOTE type="cite"> <DIV class="Section1"><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Dear Chimera’s users:</SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I have a problem to make an Amber MD movie using Chimera. I am sure I used the right Amber top file and mdcrd file, since I can use VMD to display them. In my trajectory file, I already striped water and counter-ions. Only box information was left with trajectory. However, when I display trajectory, all trajectories were out of shape. I saw the similar thing when I used VMD to display the trajectory without including PBC option. I doubt that there is something wrong with box information. But I don’t know how to fix it. Any ideas?</SPAN></FONT></P></DIV></BLOCKQUOTE>Hi Xuelin,</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>Chimera doesn't handle PBC information yet. You will have to re-image your trajectory with ptraj, as described in the "Re-imaging the trajectory back into the primary box" section of this AMBER tutorial:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><A href="http://amber.scripps.edu/tutorial/polyA-polyT_New/minandmd3.html">http://amber.scripps.edu/tutorial/polyA-polyT_New/minandmd3.html</A><BR><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> Eric Pettersen</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> UCSF Computer Graphics Lab</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> pett@cgl.ucsf.edu</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> http://www.cgl.ucsf.edu</DIV></DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV></BODY></HTML>