On Mar 8, 2010, at 11:01 AM, Francesco Pietra wrote:

Hi:

I am interested in following the pathway of a ligand forced to leave a protein. I can follow that path with the movie (NAMD format) but I would be interested to also have a trace of the pathway recorded. I would like to show around the protein the various traces for different pathways of exit of the same ligand.

Hi Francesco, One possible solution is to define a centroid at the center of your ligand at each frame. Defining centroids is only available in the 1.5 daily build. So in MD Movie's "Per-Frame" dialog you would enter "define centroid ligand". This assumes that "ligand" in fact selects the atoms of your ligand (and only those atoms), which you might want to test out beforehand with the command "sel ligand". Otherwise you might have to use a more specific atom spec than "ligand". You might also want to use some options on the 'define' command ("help define" will show those). This centroid path may be good enough as is, or you might want to show a centroid only every 5 frames or every 10 frames, in which case you would prefix the 'define' command with "#5:" or "#10:". If you want the path to be linked together rather than just a series of spheres, more work is necessary. You can save the series of centroids into a file with the "Save" button on the Axes/Planes/ Centroids tool. This will give you the coordinates of the centroid centers. You can then either create a BILD-format file (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html ) or a Chimera markers file (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/vo... ). With the former you could draw arrows, cylinders, or lines linking the coordinates, and with the latter you could make cylinder links which could then be turned into a smoothed spline path with the Volume Tracer tool. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu