Connolly surface (CONOLY)

Introduction.

If you have a copy of the Connolly surface area calculation program(s) you can use WHAT IF as an interface to these programs, and you can use WHAT IF for visualization of the results.

The Connolly program package is NOT distributed with WHAT IF. However, if you have it, you should call the PQMS and TRB executables PQMS.EXE and TRB.EXE respectively and put them in the [...VRIEND.WHAT IF.CONNOLLY] directory (/.../vriend/connolly on UNIX systems). WHAT IF will then copy them to the directory where they are needed when they are needed. The Connolly program suite holds some programs for visualization too, but these are not used by WHAT IF.

The programs by Connolly are to smart for me to understand. So I can not explain to you what they do. However, the final result is a set of dots (vertices) that are corner points of triangles that cover the surface. These dots are pairwise organized in edges. The output file of the Connolly programs that WHAT IF uses for graphical output is therefore called the vertex edge triangle file (or VET file).

The normal way of using the Connolly programs is :

1) Use PARAMS to (re-)set parameters.

2) Use MAKCON to create a coordinate input file.

3) Use RUNCON to execute the programs.

4) Use LSTCON to inspect the output files.

5) Use any of the other options to visualize the surfaces.

The output is sorted in solid bodies. A solid body is either the whole surface, or the surface of any of the cavities.

Create coordinate file (MAKCON)

The Connolly program is not a integral part of WHAT IF. WHAT IF talks with the Connolly programs via files. The coordinate file for the Connolly program (the so-called XYZR file) is written by the MAKCON option. You will be prompted for residue ranges till you give 0 (zero).

Run the Connolly programs (RUNCON)

The command RUNCON will cause WHAT IF to create all input files needed for the Connolly programs, and to execute them. This option will take up to half an hour on a PC-Iris for a medium sized protein when the default parameters are being used.

Inspecting results (LSTCON)

The command LSTCON will cause WHAT IF to show you a menu of files potentially used by the Connolly programs. Their present existence or absence is indicated. You can give the number of the file you are interested. WHAT IF will then bring that file in the editor. Give file number 0 (zero) to terminate this option.

The following files can be inspected


PQMS.INPUT       Input deck for the PQMS program
PQMS.OUTPUT      Output produced by the PQMS program
TRB.INPUT        Input deck for the TRB program
TRB.OUTPUT       Output produced by the TRB program
WHAT IF.XYZR      Coordinate file written by WHAT IF for usage by the
                 PQMS program.
WHAT IF.AREACON   
WHAT IF.AREABAC
WHAT IF.AREABCA
WHAT IF.VOLCON    File that holds per body its 'center' and the
                 surface area and volume.
WHAT IF.TRB       
WHAT IF.VET       Vertex-Edge-Triangle file. This is the final output
                 of TRB in a format that WHAT IF uses for graphical
                 visualization of surfaces/volumes.

Making a dot surface (DOTCON)

The command DOTCON will cause WHAT IF to read the VET file (see LSTCON) and put all dots it finds in a MOL-item. Every dot gets the color of the atom it is situated closest to. You will be prompted for the number of the MOL-object and the name of the MOL-item. In case there are too many dots multiple items will automatically be created.

Making a line surface (LINCON)

The command LINCON will cause WHAT IF to read the VET file (see LSTCON) and put all lines it finds in a MOL-item. Every line gets the color of the atom it is situated closest to. In case that a line is almost equally close to two atoms the color of the two atoms it is close to are mixed.

You will be prompted for the number of the solid body to be shown. You can inspect the file WHAT IF.VOLCON via the LSTCON command to see the list of available solid bodies

You will be prompted for the number of the MOL-object and the name of the MOL-item. In case there are too many dots multiple items will automatically be created.

Making a triangle surface (TRICON)

The command TRICON will cause WHAT IF to read the VET file (see LSTCON) and put all triangles it finds in a MOL-item. Every triangle gets the color of the atom it is situated closest to. In case that a line is almost equally close to two atoms the color of the two atoms it is close to are mixed.

You will be prompted for the number of the solid body to be shown. You can inspect the file WHAT IF.VOLCON via the LSTCON command to see the list of available solid bodies

You will be prompted for the number of the MOL-object and the name of the MOL-item. In case there are too many dots multiple items will automatically be created.

Making a solid surface (SOLCON)

This option only works on Silicon Graphics machines, and even on those machines it does not work very well.

The command SOLCON will cause WHAT IF to read the VET file (see LSTCON) and put all triangles solidly filled it finds in one of the four special solid objects that can be operated on by the SOL1 - SOL4 buttons in the button box at the bottom of the screen. Every solid triangle gets the color of the atom it is situated closest to. In case that a solid triangle is almost equally close to two atoms the color of the two atoms it is close to are mixed.

You will be prompted for the number of the solid body to be shown. You can inspect the file WHAT IF.VOLCON via the LSTCON command to see the list of available solid bodies

You will be prompted for the number of the solid object and the name of the MOL-item. In case there are too many dots multiple items will automatically be created.

Parameters (PARAMS)

The command PARAMS will bring you to the Connolly parameter menu. The following parameters can be (re-)set:

Radius of rolling sphere (RADIUS)

The RADIUS parameter sets the radius of the probe that is rolling over the surface. The range of valid values for the radius is 0.0 - 5.0. Values larger than 2.0 will dramatically increase the CPU time needed to execute the programs. Radius = 0.0 should be used to get the Van der Waals surface. Radius = 0.75 should be used to get cavities that can be filled by adding one carbon atom to a residue (e.g. Valine to Isoleucine). Radius = 1.4 should be used to get the solvent accessible surface.

Triangulation coarseness (ANGLE)

The parameter ANGLE determines the degree of surface triangulation. The valid range of input values is 0.3 - 3.0. The default is 1.0. If you use values larger than 1.0 the surface will be calculated faster, but will be courser. Values smaller that 1.0 will create an enormous amount of extra CPU time, but a finer surface will be created. Values between 0.7 and 1.3 are suggested.