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

[Armita Sheari]

     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