[Biojava-l] Structure alignment parameters questions

[Andreas Prlic]

Hi Shane,

If we take perhaps the three most important ones:

maxIter - the number of times dynamic programming is run.
seedRmsdCutoff -  the Rmsd cutoff for initial seeds
diagonalDistance  and diagonalDistance2 that define at which intramolecular
distance the two proteins a re compared.

There will probably some more work being done re structure alignments for
the next release, but it is a bit early to go into details.

Andreas


On Sun, Oct 4, 2009 at 7:09 PM, Shane Sturrock <
shane.sturrock at biomatters.com> wrote:

> I've started working on a plugin for Geneious to allow our users to align
> 3D PDB structures and I'm basing this on sc.align().  I've got it working
> and I've also got all the parameter defaults however there are a lot.  I'm
> looking for a bit of advice on which ones are likely to be useful to a
> typical user so I only have to put a limited set into the options panel as
> there is no need to overload them and also a pointer to where I can find the
> information on the acceptable limits for each parameter since this
> information doesn't appear in the JavaDoc.  I do have the original paper by
> Lackner et al but it would be better to know what is recommended
> specifically for the implementation in biojava.
>
> Cheers,
>
> Shane
>
> --
> Dr Shane Sturrock
> shane.sturrock at biomatters.com
> Technical Product Manager - Geneious Software
> Tel: +64 (0) 9 379 5064
> Mob: +64 (0) 21 882 482
> 220 Queen St
> Level 6 Data Centre Building
> Auckland
> New Zealand
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>