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

[Eric Pettersen]

Well, it is possible to verify an RMSD "by hand" by taking the  
individual atom-pair distances, summing their squares, and taking the  
square root of the sum.  Can be tedious if the ligand is big.  If you  
want to send me the ligand pose (and assuming you are using an  
unmodified 1A6W) I can check the RMSD.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Apr 24, 2009, at 9:58 AM, 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
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20090424/b173729b/attachment.html