Concepts introduced: reading charge files (§6.1.1), calculating electrostatic potential (§6.6.4), constructing contours (§6.4.6), coloring surfaces by potential (§6.4.13), setting the list format (§ 5.2.2).
We've probably beaten ribonuclease to death now, so we'll switch gears a little. Start spock and type fetch=1aaq.pdb.
This will contact the PDB and get the structure for HIV protease. Be patient. (If this doesn't work, have your system administrator check the script in $SPOCK/bin/getentry. This script should contact the PDB and download the file.) Once the structure has loaded, we're ready to go. Type
(or use the menu sequence Open File Charge file) to load the charge file from the library. This charge file will only charge the residues that should be fully ionized at neutral pH. You can type
to see which residues are charged. If you actually want to see the charge, we need to add that to the list format (§ 5.2.2). Type
set list format.
Fill in the prompt dialog with
Now the list command will identify the residue and print its charge and potential. Type
again to see the results. We've now verified that the molecule is charged.
At this point we'll do a simple electrostatics calculation. Choose ``Run PB solver'' under the ``Calculate Electrostatics'' menu. This will perform a electrostatics calculation using the default parameters. To see the results, let's build some contours § 6.4.6. Tear off the ``Alter Contours'' menu by selecting the dotted line at the top of it. Choose ``Add 3D contour'', and enter 1.0 for the ``Contour map at'' field, and 4 for the color. This will create a contour at +1kT and color it blue. Add another contour at -1kT and color it red (color 2). Now let's see what the effect of 1.0 M salt is on the contours. Under the ``Electrostatic parameters'' dialog of the ``Calculate Electrostatics'' menu, enter 1.0 as the salt concentration. Set the map to ``Map 2'' on the same menu, and then choose ``Run PB solver'' again. (Changing the map was so that we could keep both maps in memory, and not overwrite the first.) Build another 3D contour at +1kT, and color this one with color 10, sky blue. Depending on the orientation, you may not see any difference, because most of the high-salt contour is inside the low-salt one. Choose the ``Mesh'' display mode on the ``Alter Contours'' menu. This will show the contours more clearly. Notice, however, that the back sides of the contour meshes are white. This is the back face color. We want the mesh contours not to use the back face color, so under the ``Graphics Tie faces'' menu, choose ``3D contours''. Now you can clearly see the high-salt contour inside the low-salt one. Notice that there's little difference between the high and low salt cases in the protein interior, but the potential field doesn't extend nearly as far outwards for the high-salt case, because of the screening effects of the salt. If you want, we can hide the low-salt contour entirely at this point by choosing ``Alter Contours Change 3D contour color'', and coloring the contour at 1kT with color 4 to color 0.
We'll now make some 2D contours. Choose ``Alter Contours Add 2D contour'' and add a +1kT contour and color it with color 3 (green). Notice that as you rotate the molecule, the 2D contour lines are updated in a plane that's parallel to the screen. To set the Z value or depth of this plane, we use the clipping tool (§ 6.11.4). Call up this tool with the ``Graphics Clip tool'' menu entry. This window will have a separate menu bar. Change the setting of ``Plane type'' menu of this tool to ``Interpolation plane''. Now the slider on the left side of the clip tool window controls the depth of the 2D contour plane. Finally, we'll look at the electrostatics at the surface of the protein. Under the ``Display'' menu, turn off ``2D Contours'' and ``3D contours''. Now, build a molecular surface with the ``Alter Surfaces Build molecular surface'' menu sequence. (The default grid size and selection string are fine.) Now, we want to color the surface by the potential at that surface point. This is the job of ``Spectra'' in spock (§6.3.19), so turn on ``Spectra'' under the ``Display'' menu. The surface property spectrum will appear, but its contents are undefined at this point. Find and tear off the ``Alter Spectra'' menu. Activate the ``Set surface spectrum property'' entry of this menu, and choose the ``Vertex potential'' option. This tells spock to color the surface based on the vertex potential property. Unfortunately, this property has not yet been set, so the surface is likely to be ugly at this point. Go to the ``Calculate Electrostatics'' menu and choose ``Interpolate to atoms/surfaces''. This fills in the vertex potential fields. Finally, go back to the ``Set surface spectrum property'' entry in the ``Alter Spectra'' menu, and select ``Vertex potential'' again. This will get spock to recalculate the interpolation parameters, and the surface will be nicely colored by potential. You can read about how to manipulate the spectrum on screen in §6.3.19.
NEW: There's now a macro which does many of the steps in this tutorial automatically. It will build a surface, read a charge file, calculate the electrostatic potential field, interpolate the charge to the surface and color the surface by potential. See the macro Color_surface_by_potential.