Making 2D heat-maps of protein secondary structure

I needed to make 2D heat-maps of protein structure with time on x-axis and protein residues on y-axis. This helps to see the time evolution of structure quite nicely. This is easily accomplished by loading the trajectory in VMD and sourcing the file ss_traj.tcl and going through your entire trajectory once. This creates a buffer with all the structure information. ss_traj.tcl creates a ss_traj.dat file which has the structure information. This ss_traj.dat file is then used by ss_plot.c, after compilation of course, to generate a .ps file with the desired output. All this is explained quite well here. I made a personal copy of the files here:
ss_traj.tcl
ss_plot.c
Sample ss_traj.dat file.

Once you have the output in .ps format you can do interesting things to change the file. The 7th line has the scaling information. The width and height of the output were not to my satisfaction; so I changed the scaling factors to adjust the display. Also the executable could crash when running due to memory requirements. Simply change the dimensions of the array in ss_plot.c according to your needs.