[Biojava-l] Structure alignment parameters questions

[Andreas Prlic]

> 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 <
> shane.sturrock at biomatters.com> 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 <
>> shane.sturrock at biomatters.com> 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
>>> shane.sturrock at biomatters.com
>>> 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  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>>
>>    --
>> Dr Shane Sturrock
>> shane.sturrock at biomatters.com
>> 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
> shane.sturrock at biomatters.com
> 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
>
>
>
>
>
>
>
>
>
>