OBJECTIVE: This tutorial demonstrates how to create and display surfaces, as well as how to color surfaces by underlying atoms and atom properties.
Concepts introduced: reading PDB files (§6.1.1), Building surfaces (§6.4.5), Pre-defined residue sets (Appendix A), Distance calculations (§ 6.6.1), selection projection (§ 5.4.1), surface area (§6.6.3), surface area dots (§6.3.7).
Start spock by typing
on the unix command line. Read in the 1rnt.pdb file by either 1) typing
on the command line or 2) using the File Open PDB file menu item. (Or you could have started spock by typing spock 1rnt.pdb on the Unix command line.) Once the molecule is read in, choose the Display Surfaces menu item. Note that nothing appears to happen. This is because surfaces must be defined or built before they can be displayed. Tear off the Alter Surfaces menu. Choose ``Build accessible surface'' from this menu. Enter
(residue not water) for the atom selection and 65 in the grid dimension blanks of the prompt that appears, and press OK. The atom selection string specifies for which atoms a surface should be built, while the grid size (which is usually not changed) controls the resolution. Spock will take a few seconds to calculate the accessible surface of the molecule, and then display it in the default color (off-white, color 51).
The color of surfaces is controlled by the vc (vertex color) command. Let's color the surface by the underlying residue properties. Type
which will color surface points due to hydrophobic residues green. (I use color numbers in the 50's for surfaces because of the better contrast.) Now type
vc=54,r=basic, and vc=52,r=acidic.
The surface should now be colored according to the underlying residue polarity. Hydrophobic, acidic, and basic are all pre-defined residue sets; a full list is given in Appendix A. Note that there is overlap between the pre-defined sets, in that a residue may be all of ``aliphatic'' and ``neutral'' and ``hydrophobic''.
Let's now take a look at the substrate binding site. Choose Alter Surfaces Build molecular surface. Answer the prompt with
to surface only the amino acids. This will exclude the water molecules and the substrate. Accept the default grid spacing, if asked. Finally, since we've already constructed a surface, we'll be asked if we want to add this surface. Saying yes would create two surfaces. Choose no to replace the old surface. Rotate the view so that the substrate is in front. To increase the visibility of the substrate type
This will (in order) turn off all bonds, except the bonds in the substrate, and then make the substrate be drawn in the secondary bond mode. Type
to color any surface due to aromatic residues. Notice right off that the substrate is sandwiched between two aromatic regions of the surface.
To choose a nice single color for the entire surface, type
Let's get rid of the surface patches that aren't involved in substrate binding. We'll need to do a distance calculation (§ 6.6.1) to do this. Choose Calculate Distance Surface to atom. The ``From surface points'' prompt should be left at ``all'', but the ``To atoms'' prompt should be answered with
Spock will take a few seconds to calculate the minimum distance from each surface vertex to the substrate, and store the result in each vertex's distance property, which we can then use as a selection property. Type
Oops! We've turned off vertices within 10 Ångstroms of the substrate instead of the other way 'round. You will notice, however, that the inside of the surface is a different color from the outside. Type
to undo the last color change. Now, let's do this properly. Type
This will turn off all vertices more than 5 Ångstroms from the substrate. Rotate the view around to look at the binding pocket from all angles. Notice how deeply the base portion of the 2'-GMP is buried in the pocket. Say that we now want to know which amino acid residues make up the binding pocket. We'll need another distance calculation to do this. This time choose Calculate Distance Atom to surface, since we want to know which atoms are within a certain range of the surface. Select ``all'' atoms and enter
for the surface, to select the surface points that are currently colored. (We also could have chosen to enter vd<=5, as those are the vertices are colored.) Spock runs through the calculations in a few seconds. Now, let's see what atoms are within range of the surface. Since a typical atomic radius is about 1.7 Ångstroms, let's turn on bonds within 2 Ångstroms of the surface. Enter
Notice that there are some residues only partially drawn, because some atoms are within range, but some are not. We can remedy this situation with the command
The ``->r'' in the command means to project the selected atoms onto their residues, so that if any atom in a residue is selected, the whole residue will be selected (§5.4.1). We can now get a list of the atoms/residues involved in the surface by using the list command. Type
This will list all atoms within 2 Ångstroms of the surface. Alternately, we can type
to get a list of the currently colored residues.
Finally, let's explore the difference between the two types of surface representations in spock, ``surfaces'' and ``surface area dots''. Surface area dots are only generated when performing a surface area calculation, and there is limited control over their appearance. In contrast, the ``surfaces'' representations are fully customizable. In the Display menu, turn off ``Surfaces'' and turn on ``Surface area dots''. Then choose Calculate Volume/surface area Accessible surface area. A three-prompt dialog box will be displayed, click on ``Ok'' to accept all the default values. The dots displayed represent the accessible surface points. Accessible surface area calculations are described in §6.6.3.
Type quit to exit spock.