VMD-L Mailing List

From: madura_at_duq.edu
Date: Fri Sep 25 2009 - 15:55:05 CDT

Dear VMD Users,

  I am trying to overlay 2 structures using the information that I have
gathered from this list as well as the userguide for version 1.8.7 of
VMD. I have tried this on a windows and mac with the same results.
Here is what I am doing

mol load pdb mol0.pdb
mol load pdb mol1.pdb
set sel0 [atomselect 0 "all"]
set sel1 [atomselect 1 "all"]
measure rmsd $sel1 $sel0
set tm [measure fit $sel1 $sel0]
set move_sel [atomselect 1 "all"]
$move_sel move $tm
measure rmsd $sel1 $sel0

When I do a measure rmsd before the move the value is 33.78...

The second measure rmsd gives a value of 42.48....

Am I missing something here? I thought the two structures should have
been superimposed and the rmsd should have been close to zero. I have
attached the two pdb files. Both files are test files and contain 3 atoms
each.

Thanks in Advance for any assistance...

  Jeffry