Aims

• To reinforce the concepts of three-dimensional transformations and superposition.
• To give practice in using C libraries to construct and apply transformation matrices.
• To revise the format of ATOM records in Protein Data Bank files.

Objectives

After this practical you will:

• be able to write simple C programs that construct and apply transformation matrices.

Introduction

The example programs introduced in the lecture are in directory /users/mdstud/kemp/3Dstructure/examples

The source code for the transformation library is in file /users/mdstud/kemp/3Dstructure/src/libtransform.c

Exercises

1. Copy the example programs test_geom.c, test_centroid.c and test_fit.c into a directory of your own. Compile and run each of these programs.

2. Protein Data Bank entry 1CRN contains coordinates of two tyrosine (TYR) residues. Look at these residues in RasMol.

   1. Modify test_fit.c so that it finds the transformation matrix that fits the N, CA, C and CB atoms of the first of these tyrosine residues onto the corresponding atoms of the other tyrosine residue. What is the value of the RMS error of this fit?

   2. Apply the transformation found in part (a) to all of the atoms in the first tyrosine residue. Write out the transformed coordinates in Protein Data Bank format (see the format of ATOM records in section 9).

      View the transformed residue in RasMol. Have the residues been superposed?

   3. Modify your program so that it superposes the first tyrosine residue onto the second using all atoms to perform the fit. What is the value of the RMS error of this fit?

3. Modify the program written in question 2 to compare the active sites (residues His57, Asp102 and Ser195) of two serine protease enzymes e.g. Protein Data Bank entries 1TLD, 3BTK 1EZX (see questions 5, 6 and 8 of the Molecular Graphics 1 practical).