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

[Michael Mysinger]

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")?
>> >
>> > 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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