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Structure alignment parameters questions
by Shane Sturrock
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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@... 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@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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Re: Structure alignment parameters questions
by Andreas Prlic-3
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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@...> 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@... > 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@... > http://lists.open-bio.org/mailman/listinfo/biojava-l > Biojava-l mailing list - Biojava-l@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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Re: Structure alignment parameters questions
by Shane Sturrock
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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@... > > 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@... > 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@... > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Dr Shane Sturrock shane.sturrock@... 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@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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Re: Structure alignment parameters questions
by Andreas Prlic-3
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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@...> 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@...> 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@... >> 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@... >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > -- > Dr Shane Sturrock > shane.sturrock@... > 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@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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Re: Structure alignment parameters questions
by Shane Sturrock
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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@... > > 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@... >> > 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@... >> 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@... >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > -- > Dr Shane Sturrock > shane.sturrock@... > 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@... 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@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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Re: Structure alignment parameters questions
by Andreas Prlic-3
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> 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@...> 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@...> 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@... >>> 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@... >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> >> >> -- >> Dr Shane Sturrock >> shane.sturrock@... >> 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@... > 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@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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Re: Structure alignment parameters questions
by Shane Sturrock
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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@... >> > 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@... >>> > 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@... >>> 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@... >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> >> -- >> Dr Shane Sturrock >> shane.sturrock@... >> 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@... > 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@... 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@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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