Quick tour
Basic installation
First of all, you need to download the VMD plugin.
Decompress it and follow the instructions in the README file :
Installation troubleshoutings
First steps with Pck
- load a molecule in VMD
- In the VMD menu, select the "pocket analysis" item
- Specify the vmd-molid
of the vmd-molecule
in which you want to detect pockets
- Launch computations
...A bit further
- You can use the selection field to restrict the pocket detection to a
subset of atoms in your vmd-molecule. The selection query is sent to VMD,
it can be any vmd selection query, for exemple : "all", "protein",
"all and not water"...
- You can modify the probe radius (defaults at 1.4 Angstrom, the radius
of a water molecule)
- You can change the detection algorithm to switch from closed pockets (default)
to wide opened pockets.
User manual
Choose VdW radii
Choose detection algorithm
