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MAPS
 
MAPS
MAPS (which stands for Multiple Alignment of Protein Structures) is an automated program for comparisons of multiple protein structures. From several homologous proteins with common structural similarities, the program can automatically superimpose the 3d models, detect which residues are structural equivalent among all the structures and provide the residue-to-residue alignment.The structurally equivalent residues are defined according to the approximate position of both main-chain and side-chain atoms of all the proteins. According to structure similarity, the program calculate a score of structure diversity, which can be used to build a phylogenetic tree. For detailed descriptions about how it works, please see the reference paper)

MAPS runs on Linux machines s; the executable is in:

/joule2/programs/maps or just type "maps"

The local documentation is in:

file:///joule2/programs/maps/maps.html

or from the author's web site at

http://bioinfo1.mbfys.lu.se/TOP/maps.html 

The program MAPS will calculate an RMSD for you
and output a new pdb file with the second molecule
superimposed on the first molecule.

Here is an example script file:

#!/bin/csh -f
cat > t.inp << END
method 1
cbeta 45 80
topfit yes
pdb actxtalb.pdb xtal 
pdb holmes2003b.pdb holmes
match rate 0.35 0.8
residue 3
distance 3.8
write yes
END
maps < t.inp

Edit the script in two places:
There are two lines that begin with "pdb"
Following the first "pdb" put the name of the PDB file of your reference molecule then
a short description of the molecule.
Following the second "pdb" put the name of the PDB file of the moving molecule then
a short description of this molecule.

Then just run the script.
You should get an output file with the superimposed coordinates
of the second molecule.

Screen output will tell you the RMSD and the number of
alpha carbons superimposed.

For documentation, see
http://bioinfo1.mbfys.lu.se/TOP/maps.html