Hi Francesco, On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote:
If at all, I did not understand if a continuous trace of the centroid (instead of a series of balls) can be obtained in the context of the protein. That would improve the presentation further. Otherwise, the series of balls for the centroid, with appropriate choice of radius and step size, shows the pathway of the ligand through the protein adequately.
Nothing simple comes to mind. One way that's a bit of work would be to save the centroid information to a file (the 'Save' button on the Axes/Planes/Centroids interface) and the use a text editor to create a BILD file (BILD format) showing lines/cylinders connecting the centroid centers.
As a minor point, I was unable to render helices transparent. Transparency would help to to see the centroid trajectory in between helices.
Should be possible unless there's something wrong with your graphics cards. Try this: Select->Structure->secondary structure->helix Actions->Color->from editor This will bring up a color editor. Try making a transparent red. For me, the editor looks like this when I do that: (note the "Opacity" box is checked) and the structure looks like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
