[Dock-fans] different RMSD calculated with Dock and Chimera

[Michael Mysinger]

Is one using heavy atoms only and the other using all atoms?

Cheers,
Michael Mysinger

Ben Keshet wrote:
> Hi Dock fans,
>
> I have a ligand pose generated by Dock (grid score) with a calculated 
> rmsd of 0.92 angstrom from a crystallized pose (PDB code 1A6W). However, 
> when I visualize the docked pose and the crystallized ligand using 
> Chimera, and calculate the rmsd using the command line (e.g. rmsd #1 
> #2), I get 1.591 angstrom. The atoms numbering is identical between the 
> two structures. While this may be a small difference, percentage-wise it 
> is pretty big.
>
> Did anyone encounter differences in rmsd calculation between Dock and 
> Chimera, or other software? Does anyone know what could cause this 
> difference (and which one is "true")?
>
> Thanks,
> Ben Keshet
> UMBC
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