[Biojava-l] Structure alignment parameters questions

[Shane Sturrock]

Ah ha, I got pretty close with my guesses for which I had:

maxiter: 1-10 (didn't think there was any point in having 0 iterations  
but I guess you know better than me)
seedRmsdCutoff 0.5 - 10.0 (I thought about starting with 1.0 but took  
it a little further down, and 10 was higher than I figured it would  
ever need to be)
diagonalDistances 1 - 20 (so pretty close again).

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.

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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
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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
>
>
>
>
>
>
>
>
>
>

--
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