I'm sure 1.7 is lightyears better but 1.5 is what I was told by our
team here is the one I should be using. I've got something that runs
at the moment and I'll try the 1.7 version and see how that goes.
One problem I am having at the moment is a lack of
InterruptedException which would be helpful so I can cancel an
alignment cleanly. As it stands I can cancel the Geneious part of it
but the alignment will continue in the background. If that has
changed in 1.7 then that would make a good case for switching.
Shane
On 8/10/2009, at 5:09 PM, Andreas Prlic wrote:
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
--
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
