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

[Ben Keshet]

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