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

[Scott Brozell]

Hi,

Science is for everyone - so everyone can vote.

:)
Scott 

On Thu, Apr 30, 2009 at 03:09:04PM -0400, Ben Keshet wrote:
> I am not sure who gets to vote, but I agree that changing the tag in the 
> mol2 files makes most sense.
> 
> Thanks,
> Ben
> 
> Scott Brozell wrote:
> >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
> >>>-------------- next part --------------
> >>>An HTML attachment was scrubbed...
> >>>URL: 
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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")?