[Dock-fans] Dock-fans Digest, Vol 59, Issue 21; rmsd vote

[Scott Brozell]

Hi,

Note that the manual correctly documents the rmsd as heavy atom:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileInput

We could change the tag in the mol2 files from
########## RMSD:
to
#HEAVY ATM RMSD:

This is preferable to changing the dock input name: calculate_rmsd
But the tradeoff is still with backward compatibility.
In a strange spirit of democracy, I invite a vote.

Scott

On Tue, Apr 28, 2009 at 02:00:10PM -0700, Michael Mysinger wrote:
> 
> In addition to what John and Eric said, it is important to remember that 
> the X-ray crystal structures themselves have both measurement and 
> modelling errors, such that we are much more confident in the 
> experimental positions of the heavy atoms than in the positions of the 
> hydrogen atoms. For all of the these reasons, we typically use heavy 
> atom only RMSDs.
> 
> Cheers,
> Michael Mysinger
> 
> Ben Keshet wrote:
> > I calculated the RMSD "manually" (actually with a spreadsheet), by 
> > taking the root of the average of the squared atom-atom distances. The 
> > value I got with all the atoms included is 1.531A, which is close 
> > enough to the Chimera value of 1.529. If I omit the hydrogens and 
> > include only heavy atoms, I get 0.852A, which is the value I have on 
> > the Dock mol2 output file. I got a similar result with another pair of 
> > ligands. So I am guessing that Dock is using only the heavy atoms for 
> > RMSD calculation, is that correct? Thanks, Ben Message: 5 Date: Fri, 
> > 24 Apr 2009 10:02:31 -0700 From: Eric Pettersen <pett at cgl.ucsf.edu> 
> > Subject: Re: [Dock-fans] different RMSD calculated with Dock and 
> > Chimera To: Ben Keshet <keshet1 at umbc.edu> Cc: dock-fans 
> > <dock-fans at docking.org> Message-ID: 
> > <D6911B1B-6D3F-4ABB-BB57-DA3E16378452 at cgl.ucsf.edu> Content-Type: 
> > text/plain; charset="us-ascii" 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
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> > ------------------------------
> >
> > Message: 6
> > Date: Fri, 24 Apr 2009 10:40:29 -0700
> > From: "Michael Mysinger" <Michael.Mysinger at ucsf.edu>
> > Subject: Re: [Dock-fans] different RMSD calculated with Dock and
> > 	Chimera
> > To: "Ben Keshet" <keshet1 at umbc.edu>
> > Cc: dock-fans <dock-fans at docking.org>
> > Message-ID: <49F1F98D.9050800 at ucsf.edu>
> > Content-Type: text/plain; charset=iso-8859-1; format=flowed
> >
> >
> > Is one using heavy atoms only and the other using all atoms?
> >
> > Cheers,
> > Michael Mysinger
> > 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")?