**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.

Tue Sep 14 16:44:48 CDT 1999