modeling

MSMS is a great piece of software for rapidly calculating molecular surfaces. You can find it here: http://mgltools.scripps.edu/packages/MSMS

SCWRL does a great job at optimizing rotamers to avoid clashes, but it doesn't allow you to make customizations. VMD's Mutator plugin will allow you to mutate an amino acid to a different amino acid, but not change the rotamers, and MODELLER will allow you to model the rotamers but only using restraints and very specific torsional angles.

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.
   

Most of these methods are based on the Shrake-Rupley algorithm [1] which creates many points on the surface of each (heavy) atom and determines whether each point is occluded or exposed to solvent.

You can calculate SASA in VMD's tkConsole with the measure command using the following syntax:

measure sasa  $selection [-points varname] [-restrict restrictedsel] [-samples numsamples]

Here is some Java code for calculating the principal axes of a molecule and orienting it starting from a PDB file of atom coordinates. I wrote this implementation first in Java based on the Tcl/Tk-based Orient script written by Paul Grayson for VMD. I will re-write this in Python and post that version soon.

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.