VMD-L Mailing List

From: Mikolai Fajer (mfajer_at_gmail.com)
Date: Thu Aug 25 2005 - 07:09:33 CDT

The "measure fit" command in VMD will calculate the 4x4 transformation
matrix to fit one atom selection to another. If you want to overlay
two drug molecules on the basis of three or four atoms, first create a
atom selections with those atoms for each molecule.

set base_original [atomselect 0 "index 1 to 4"]
set base_new [atomselect 1 "index 1 to 4"]

These Tcl commands take a few things for granted. One, that the
original drug molecule is loaded into the first molid and the new drug
molecule is loaded into the second molid. Two, that the atom id's for
your basis are 1, 2, 3, 4. Change to reflect your situation. Then
calculate the transformation matrix and apply it to the entire new
drug molecule.

set matrix [measure fit $base_new $base_original]
set new_drug [atomselect 1 "all"]
$new_drug move $matrix

That should do it! 

-- 
     -Mikolai Fajer-