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

[John J. Irwin]

Hi Ben

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?
That sounds right to me.  We would normally not use protons in an RMSD
calculation.

John

> 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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