[Chimera-users] Visualising tunnels by MolAxis

[George Tzotzos]

I’ve tried to visualise protein binding site tunnels to the bulk solvent as detailed in the instructions given in:

http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html

The problem I encounter is that I cannot align tunnel produced by _graph_pathway_0_all build file to the receptor. In other words, the coordinates of the receptor and the tunnel are different.

Is there a way of doing this?  

Thanks in advance for any help.

Regards

George