Assignment 1: visualization and ranking of protein conformations  (Page 2/5)

Familiarize yourself with the capabilities of VMD through its documentation , especially the User's Guide and various tutorials.

Start by visualizing the native conformation of the protein in 1COA.pdb. You can do so by selecting the "File/New Molecule" option in the "VMD Main" window. This will pop up the "Molecule File Browser" window. Browse through your files to find the file you downloaded from the PDB website and click "Open." Make sure the "Determine File Type" pulldown menu is set to "PDB," then click "Load."

You will note that the default graphical rendering represents bonds between atoms as lines. You can change the grpahical representation of the molecule loaded through the "Graphics->Representation" menu option in the "VMD Main" window. Note that, by default, VMD selects all atoms for drawing. Please get familiar with the "Draw Style" options by experimenting with the "Coloring Method" and "Drawing Method" pulldown menus. One useful drawing method is the cartoon representation, which draws α-helices as cylinders and β-sheets as flattened arrows. You can further exmphasize these secondary structure elements by choosing the "Structure" option under "Coloring Methods." You should be able to see something like Figure 1 below. You can save your rendering as an image through the "File->Render" option.

A. visualizing a set of conformations

Now it's time to look at more than one conformation. VMD supports reading of cartesian coordinates in multiple formats. We will use crd files from now on. A crd file contains one dummy line followed by a list of conformations, where each conformation is specified as alist of 3N coordinates for a protein of N atoms. There are other formats in which to store conformations, e.g. dcd files. Though they occupy less space because they store conformations in binary format,it is easier for you at this point to use crd files which store conformations in ASCII. VMD allows you to do i/o, i.e. you can read acrd file through VMD or write out the coordinates of a conformation to a crd file. Try VMD's output capabilities by writing out the nativeconformation specified in the pdb file for 1COA that you have already loaded at this point. Click with the mouse at the line that specifiesthe molecule you have loaded - this action will highlight it in yellow. Then follow the "File->Save Coordinates" option. At the new popped-up window, select the molecule for which you want to write outthe coordinates (this should be 1COA), choose the crd file format, choose 0:0 for the beginning and end of the frames to be written out,and save the coordinates to a new crd file, e.g. "1COA_native.crd."

In this assignment, you will be required to analyze conformations of 1COA. Since the file provided by the Protein Databank does notcontain all atoms (hydrogen atoms are usually not reported in crystallographically-determined structures), we will be using a more complete version of the native conformation with the hydrogen atoms reconstructed: 1COA_native.pdb, included in the .zip archive linked at the top fo the page. Make sureto use this .pdb file from now on.