Hi Sharon, It seems to me that there are some issues with this. In particular you need the helices you are measuring to maintain their helicity throughout the trajectory otherwise you will get meaningless angle values for frames with poor helicity (the computed axis direction will be fairly random). Also, to identify the helixes there have to be specific residues that always participate in the helix -- which I imagine would usually be the case but I can envision scenarios where a helix winds/unwinds up and down a sequence. Within those constraints, you can measure an inter-helical angle with the Python script I've attached. You would use it in MD Movie's Per- Frame->Define Script dialog (choose "Python" in "Interpret script as"). You would need to change the specific residue numbers in the script to correspond to the "core" (non-unraveling) resides of your helices. The angles will be printed to the Reply Log as the trajectory plays. Let me know if you have any questions/problems. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 14, 2009, at 10:38 AM, Shuanghong Huo wrote:

Dear Chimera Developers,

My group needs to calculate the inter-helical angle for a large trajectory. We know Chimera can calculate the inter-helical angle for a conformation. We are wondering what the easiest way to use Chimera to process the whole trajectory. It is amber trajectory.

Thanks, Sharon Huo, Ph.D. Associate Prof. of Chemistry & Biochemistry Clark University