[Dock-fans] Dock-fans Digest, Vol 59, Issue 21

[Eric Pettersen]

The heavy-atom RMSD would seem more informative in this case.  You  
probably don't care about methyl group rotations for instance.  Also,  
the all-atom RMSD maybe be misleadingly high since the protons are  
paired by name, not by position -- so a methyl group may actually  
match quite well spatially but give a high RMSD because the atoms  
(when paired by name) aren't close.

--Eric

On Apr 28, 2009, at 5:52 AM, 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")?
>> >
>> > Thanks,
>> > Ben Keshet
>> > UMBC
>> >
>> > _______________________________________________
>> > Dock-fans mailing list
>> > Dock-fans at docking.org
>> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>>

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