On Sep 5, 2007, at 10:37 AM, Wang, Xuelin wrote:

Dear Chimera’s users:

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? Hi Xuelin, 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:

http://amber.scripps.edu/tutorial/polyA-polyT_New/minandmd3.html --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu