[Biojava-l] Structure alignment parameters questions

[Shane Sturrock]

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