Hi Shane, so again with the disclaimer that things probably will change, for now I recommend the following ranges : maxiter: 0 - 10 seedRmsdCutoff 1.0 - 5.0 diagonaldistances: 1-15
On Tue, Oct 6, 2009 at 1:40 PM, Shane Sturrock < [email protected]> wrote: > Hi Andreas, > That sounds perfect as it keeps the options panel nice and compact. Do you > have a recommendation for the range (min to max) of settings for each of > these options? > > Shane > > On 6/10/2009, at 5:58 PM, Andreas Prlic wrote: > > 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 >> > > > -- > 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
