Tips on Calculating RMSD

[Andrew Orry]

There are a number of ways to calculate RMSD and the method you use
depends on the problem you wish to solve. For example you need to use
different approaches when calculating the RMSD of proteins and
ligands.

There are two options in GUI:

1. Tools/Analysis/RMSD # For protein structures only.
http://www.molsoft.com/gui/rmsd.html
2. Superimpose Button # will work for chemicals and protein structures
but beware the ligand is superimposed and therefore not useful for
comparing docked structures
http://www.molsoft.com/gui/superimpose.html

Command Line:

1. RMSD command
http://www.molsoft.com/man/icm-functions.html#Rmsd
2. Static RMSD command # the way to compare two docked structures -
use the chemical parameter and beware of how many atoms have been
compared when comparing non-identical chemical structures.
http://www.molsoft.com/man/icm-functions.html#Srmsd