[Biojava-l] Structure alignment parameters questions

[Shane Sturrock]

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 <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
>
>
>
>
>
>
>
>
>
>

--
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