[Biojava-l] [Biojava-dev] How can I calculate the RMSD of Global Alignment?

[Armita Sheari]

Dear Andreas,
 
Thanks for your answer. I saw the run of the example you had linked. As I found, all rmsd numbers which were calculated in the example were related to Local Alignments. Wheares I need to find the RMSD of Global Alignment (without any Gap). And we should consider all Alpha Carbons of the proteins to calculate the RMSD. 
 
Which parameters should I change in align method to reach the Global Alignment with NO Gap?
 
Thanks again,
ArmitaSh


--- On Thu, 12/25/08, Andreas Prlic <andreas.prlic at gmail.com> wrote:

From: Andreas Prlic <andreas.prlic at gmail.com>
Subject: Re: [Biojava-dev] How can I calculate the RMSD of Global Alignment?
To: armita_sh at yahoo.com
Cc: "Biojava" <Biojava-l at lists.open-bio.org>, "biojava-dev" <biojava-dev at biojava.org>
Date: Thursday, December 25, 2008, 7:20 PM

Hi Armita,

I agree the missing documentation for all the alignment parameters is
a problem...   It is not exactly clear from your mail what is the
problem you encountered. The code that you sent in principle looks
fine. I suspect you want to select the "best" of the alternative
alignments? In that case you can simply take the first, since the
alignments come out sorted. An example can be run from here:

http://www.biojava.org/download/performance/biojava-structure-example1.jnlp

The alternative alignments are sorted according to their number of
structurally equivalent residues. The rmsd in the different
alternative solutions is always kept under a certain threshold (one of
the parameters), since one of the strategies is to try to keep the
rmsd constant, while maximizing the number of structurally equivalent
residues. Similar results are clustered together in the same cluster.
In the example shown above this allows to find the multiple matches
between the four chains of hemoglobin and myoglobin.

Andreas





On Wed, Dec 24, 2008 at 6:02 PM, Armita Sheari <armita_sh at yahoo.com>
wrote:
>      Hi everyone,
>
>  I want to calculate the RMSD relevent to the Structural Global Alignment
of two proteins. I have used the align method of the StructurePairAligner class
with default parameters, and then I have calculated the RMSD using the getRmsd
method of the AlternativeAlignment class. But it seems something is wrong.
> I think I should change some parameters of align method which are defined
in StrucAligParameters class. Unfortunately, I couldn't find any
documentation that describes the parameters (not in the api nor in the source
code).
>
> I would be thankful if you take a look at my code and let me know your
opinion about which parameter(s) I should change.
>
> StructurePairAligner structurePairAligner = new StructurePairAligner();
> structurePairAligner.align(structure1, structure2);
> AlternativeAlignment[] alternativeAlignment = 
structurePairAligner.getAlignments();
> ClusterAltAligs.cluster(alternativeAlignment);
>
> double minRmsd = 1000;
> double rmsd = 0;
> for(int i = 0; i < alternativeAlignment.length; i++)
>            {
>                rmsd = alternativeAlignment[i].getRmsd();
>                if(rmsd < minRmsd) minRmsd = rmsd;
>                rmsd = 0;
>            }
> return minRmsd;
>
> Thanks,
> Armitash
>
>
>
>
>
>
>
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