From: John Stone (
Date: Fri Sep 25 2009 - 22:17:31 CDT

  There's a bug in the alignment code for the 3 atom case, if you
select 4 or more atoms, it should be fine. Sorry about this, it's
on the fixit list...

  John Stone

On Fri, Sep 25, 2009 at 04:55:05PM -0400, wrote:
> 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

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