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 < [email protected]> 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 > [email protected] > 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 - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
