[Biopython-dev] RMSD calculation

[George Devaniranjan]

Hi,
Thank you- I have been noticing that for most PDB-superimposer well as
SV-superimposer give similar values
In addition PYMOL in most cases also gives similar values however in all
cases VMD continues to give the smallest value.

I will also test ProFit -thanks for the link.
George

On Tue, Nov 2, 2010 at 9:17 AM, Christian Schaefer <schaefer at rostlab.org>wrote:

> Hey,
>
> I was using the PDB superimposer once and compared it to ProFit [1] which
> does a McLachlan fitting. Both return essentially the same rmsd, while the
> implementation in Bio.PDB seems to yield higher precision.
>
> Chris
>
> [1] http://www.bioinf.org.uk/software/profit/
>
> --
> Dipl.-Bioinf. Christian Schaefer
> Technical University Munich
> Department for Bioinformatics
> Faculty of Computer Science/I12
> Boltzmannstr. 3
> D-85748 Garching b. Muenchen
> Germany
> http://www.rostlab.org/~schaefer <http://www.rostlab.org/%7Eschaefer>
>
>
>
> On 10/30/2010 01:42 AM, George Devaniranjan wrote:
>
>> Thanks Eric and Peter,
>> Your patience in answering this question is very much appreciated.
>> I think Eric maybe right, I tried the RMSD calculation for several
>> structures and VMD does give a lower value for them all.
>> George
>>
>> Thanks once again for all of you for your answers
>>
>> On Fri, Oct 29, 2010 at 10:39 PM, Eric Talevich<eric.talevich at gmail.com
>> >wrote:
>>
>>  On Thu, Oct 28, 2010 at 12:49 PM, George Devaniranjan<
>>> devaniranjan at gmail.com>  wrote:
>>>
>>>  I was wondering why there is two functions for calculating RMSD
>>>>
>>>> 1)in the SVDSuperimposer()
>>>> 2)in PDB.Superimposer()
>>>>
>>>> In the code its says RMS-is RMS being calculated instead of RMSD???
>>>> I ask because VMD gives a different value for RMSD to the one from
>>>> Biopython
>>>>
>>>>
>>>>  Hello George,
>>>
>>> Here's my understanding of it:
>>>
>>> 1. RMSD and "RMS distance" both mean root mean square deviation, in terms
>>> of the distances in 3D space between each corresponding pair of atoms.
>>> The
>>> RMSD between all atoms in two aligned structures may be different than
>>> the
>>> RMSD between backbone atoms only. Or, if the two structures don't have
>>> the
>>> same peptide sequence, that raises another set of issues.
>>>
>>> 2. In Biopython, PDB.Superimposer internally uses SVDSuperimposer. It's a
>>> simplified wrapper.
>>>
>>> 3. The SVDSuperimposer module allows you to either (i) align two
>>> structures
>>> in 3D space and then calculate RMSD, or (ii) just calculate RMSD without
>>> spatially (re-)aligning the structures. PDB.Superimposer just does the
>>> former. If the structures weren't already aligned, these can yield very
>>> different values.
>>>
>>> 4. There are many ways to perform a structural alignment; SVDSuperimposer
>>> implements a simple one. PyMOL, VMD, ce, DALI, and other programs
>>> implement
>>> more advanced methods.
>>>
>>> So don't be alarmed that VMD gives you a smaller RMSD than
>>> PDB.Superimposer
>>> -- it just means VMD found a better alignment between the two structures.
>>>
>>> Best,
>>> Eric
>>>
>>>
>>>
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