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
