vmd

I am no expert in this field, but I have found two major methods related to simplifying a three-dimensional object: reverse subdivision and decimation/reduction. Both of these methods can be applied to both surfaces and volumes.

1. Open the two structures:
   

   vmd -m structure1.pdb structure2.pdb

2. Open the RMSD Calculator (NOT the RMSD Trajectory Tool):
   Extensions > Analysis > RMSD Calculator
   You can use the Trajectory Tool to align structures too, but the Calculator actually changes the coordinates of the aligned structure so that you can save them, while the Trajectory Tool only changes the orientation of how the two molecules are displayed with respect to one another.
3. Specify the atoms you want to use in the text box in the upper left corner of the RMSD Calculator.
   

I promise that was the only time I will shout on this blog.

There are instructions below for building alpha-helical peptides. You can also use the on-line Helix Builder to construct helices. It uses the same method.

I recently came across several VMD users who were not aware of the VMDRC startup script. Before configuring my vmdrc, the first two years of using VMD, I had been turning off the XYZ axis arrows every time I started VMD. I would also always switch from perspective to orthographic mode, and often switch to a white background from the black. Also, since I have a graphics card I was always switching to the GLSL rendermode. These are all things that can be specified automatically in the startup script file.

I couldn't remember changing anything, but coming to the office one morning I began to receive the following error when trying to start VMD:

"Error: Unable to create openGL window."