Actually I would like to do some movie with chimera but I never used before. I have two crystal structure of two different conformation of the protein that I work with. I would like to see the trajectory from conformation 1 to 2. I just downloaded the chimera but I don't know how to start.

Could you tell me how to make the movie? I would appreciate you help. Is that possible to load molecule 1 and 2 and see how the trajectory is ?

Begin forwarded message: From: Elaine Meng <meng@cgl.ucsf.edu> Date: November 30, 2007 10:29:41 AM PST It sounds like you want to use the Morph Conformations tool (under Tools... Structure Comparison). If you have two structures, it will "make up" a series of in-between structures to create a trajectory. You have to match (superimpose) the two structures yourself first. There are different options of how to make the in-between structures and how many to make. The trajectory-viewing tool, MD Movie, is automatically started to show the trajectory. From MD Movie you can record the trajectory as a movie file (Quicktime or other formats) or just save it as a PDB file for later viewing in Chimera. Probably you will need to learn a little bit about using Chimera so that you can set the display (ribbons, background color, displaying important sidechains) how you want for the movie. Chimera comes with a User's Guide. You can open it directly or search it from the Chimera Help menu. Also clicking the Help buttons on dialogs will automatically open the corresponding man pages. I will give some links to our Web site, but most of the same pages are included with your download. Tutorial on matching structures and making nice images: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html Manual page for Morph Conformations: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html for MD Movie: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (see the "Recording a Movie" section) For basic Chimera use, there is "Getting Started" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html and a more detailed version of that at our web site (not in the User's Guide): http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html but if you get stuck or have trouble finding something, you can ask me about it. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html