Volume of te active site of ptotein #4
Description
Dear Experts,
I am using 'volarea' to calculate the active site volume of protein in vmd. I select the active side as follows:
I consider a sphere of radius 8 angstroms from Zn as a center. I visualize the active site in VMD as "all within 8 of name ZN". I am trying to calculate the volume of the selected residues ("all within 8 of name ZN").
- open VMD
- Extensions
- Porto biochem
- I select volume calculation
In volarea interface, where do I put this selection ("all within 8 of name ZN")? There are two selection options. One is global selection, and another is specific selection.
Is "atom volume calculation" on or off?
There are two other options 1) scale and 2) cavity probe radius. How can I set the radius of the sphere (8 angstroms)?
Thanking you.
With regards,
Dulal Mondal