> maxiter: 1-10 (didn't think there was any point in having 0 iterations but > I guess you know better than me) >
0 is quick and dirty... > Thanks anyway, I'll use your recommendations. For the moment, we'll stick > with the version in Biojava 1.5 but will keep an eye on developments. > you mean 1.7, right? 1.5 is ancient and I can;t recommend using that... http://biojava.org/wiki/BioJava:Download Andreas > > Shane > > On 8/10/2009, at 4:55 PM, Andreas Prlic wrote: > > 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 >> >> >> >> >> >> >> >> >> >> > > -- > 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
