OBJECTIVE: This tutorial will demonstrate how to use some of spock's calculation facilities, in particular, how to calculate various surface areas.
Concepts introduced: surface area calculations (§ 6.6.3) There are two different types of surface area calculations in spock: atom based and surface based. Atom-based surface areas compute the surface area by constructing a pointwise representation of the surface, where each point represents a small patch of surface which may potentially contact water. The areas of these patches are summed to give the total area, and the area per atom. Surface-based surface areas require a pre-existing 3D surface to be calculated, and the area is simply the sum of areas of the triangles on that surface.
Start spock and read in our old friend, 1rnt.pdb. Let's first calculate the accessible surface area of the protein.
Choose the ``Calculate 
Volume/surface area'' menu, and tear
it off. Click on ``Probe radius''. The probe radius represents the
radius of the water molecule that we're going to mathematically roll along
the surface of the molecule. Since 1.4 is an appropriate value, just
click Ok to accept it, but you could change it if you want. Now click on
``Probe resolution'', and change that value to 2. The resolution
indicates how many times to subdivide an icosahedron for the probe, and
thus determines the number of points used in the test sphere as described
in §6.6.3. Choosing 2 results in a test sphere of
320 points, which is quite sufficient. Increasing the number further
really only increases the time the calculations take without adding any
accuracy.
Now that the parameters are set, let's actually do the calculation.
Choose ``Calculate Volume/surface area
Accessible surface area''. When prompted, enter
| Surface atoms | r<>0 |
| In context of | none |
| Color | 5 |
i.e. not water for the atoms, ``none'' for ``in context of'' and ``5'' for the surface area dots color. If the ``Surface area dots'' object is turned on in the ``Display'' menu, then a dot at each accessible probe point will be displayed in this color. Press ``Ok'' to do the calculation. The surface area is given in units of square Ångstroms. Spock reports the total accessible surface area for all atoms. What we want is a per-atom breakdown of the results. To accomplish this, we'll use the list command, but the surface area isn't included in the default information supplied by list. Change the list format with the command
set list format
and fill in the prompt:
| List format | * |
| Variable list | id,sa |
i.e. * for unformatted output in the ``format'' field, and id,sa in the ``Variable list'' field to request the identity and the surface area. Now type
list
to see the per-atom surface area results.
Go ahead and turn on ``Surface area dots'' in the ``Display'' menu to see the results graphically.
Suppose we wish to know what parts of the substrate are buried (solvent inaccessible). We could, in principle, construct the solvent accessible surface, and look to see which atoms are on the surface, but that only gives a qualitative answer. A better solution is to calculate the exposed surface area directly with an accessible surface area calculation. First, reset all the surface areas to 0 with the command set sa=0
Now, choose ``Accessible surface area'' from the Calculate
Volume/surface areas'' menu, and enter
| Surface atoms | r=substrate |
| In context of | m=1,r<>wat |
| Color | 5 |
This tells spock to calculate surface for the substrate atoms, with atoms in molecule 1 taking up space as well-no surface is calculated for atoms in molecule 1, but they are still used to bury other atoms; they still take up space. Press ``Ok'' to do the calculation, and type
list,r=substrate
to see the results. Those atoms which still have a zero for the surface area are buried.
Finally, let's say we wish to know the area of a constructed surface. Type
makesurf,r=aa
to make the molecular surface of the protein. Now choose ``Area of
constructed surface'' from the Calculate Volume/surface
areas menu. Accept all as the default, and spock will print out the
sum of the areas of the triangles making up the surface.