[Biojava-l] Structure alignment parameters questions

[Andreas Prlic]

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
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>
>
> --
> 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
>
>
>
>
>
>
>
>
>
>