[Biojava-l] Structure alignment parameters questions

[Shane Sturrock]

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