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

[Ben Keshet]

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
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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")?
>>>>>           
>
>