Thanks Daniel!

I will have a look at the example and wiki. Davide

On Feb 1, 2011, at 7:25 PM, Daniel Russel wrote:

> Check out the ConnectivityRestraint. It is very general, so not the easiest thing to use though. There is an example at http://salilab.org/imp/nightly/doc/html/core_examples.html (for some reason the links from classes to the examples using them are broken at the moment). > > There is also a wiki page talking about the various options: http://salilab.org/imp/wiki/Ambiguity > > > On Feb 1, 2011, at 9:18 AM, Davide Bau wrote: > >> Hi everyone, >> >> I need to implement a conditional restraint to account for multiple copies of the same particles in my data set, ie to account for interaction ambiguity. Are conditional restraints implemented in IMP? >> >> Thanks! >> Davide >> >> >> -- >> Davide Baù >> Structural Genomics Unit >> Bioinformatics & Genomics Department, Prince Felipe Research Center >> Avda. Autopista del Saler 16, 46012 Valencia, Spain >> Tel: +34 96 328 96 80 (ext. 1004) Fax: +34 96 328 97 01 >> email: dbau@cipf.es web: http://bioinfo.cipf.es/dbau/ >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users

Some of what is covered on the wiki page includes things that could easily be done but are not, including that. Elina is currently working on a much more powerful and flexible replacement for the current implementation. For the time being, the easiest way to get that would be to implement a PairScore that gives such edges a very large score and passes all other edges off to what ever pair score you would normally use. They will then be effectively disallowed. There is an example pair score in the examples module (it should be in C++ for efficiency reasons).

On Apr 4, 2011, at 7:25 AM, Davide Baù wrote:

> Hi list, > > I was having a look at the ambiguity wiki page (http://salilab.org/imp/wiki/Ambiguity). It states that certain edges can be explicitly disallowed, but I was able to find a method to do it in the ConnectivityRestraint doc page. It it possible to disallow certain edges or is it a functionality not yet implemented? > > Regards, > Davide > > > On Feb 1, 2011, at 7:25 PM, Daniel Russel wrote: > >> Check out the ConnectivityRestraint. It is very general, so not the easiest thing to use though. There is an example at http://salilab.org/imp/nightly/doc/html/core_examples.html (for some reason the links from classes to the examples using them are broken at the moment). >> >> There is also a wiki page talking about the various options: http://salilab.org/imp/wiki/Ambiguity >> >> >> On Feb 1, 2011, at 9:18 AM, Davide Bau wrote: >> >>> Hi everyone, >>> >>> I need to implement a conditional restraint to account for multiple copies of the same particles in my data set, ie to account for interaction ambiguity. Are conditional restraints implemented in IMP? >>> >>> Thanks! >>> Davide >>> >>> >>> -- >>> Davide Baù >>> Structural Genomics Unit >>> Bioinformatics & Genomics Department, Prince Felipe Research Center >>> Avda. Autopista del Saler 16, 46012 Valencia, Spain >>> Tel: +34 96 328 96 80 (ext. 1004) Fax: +34 96 328 97 01 >>> email: dbau@cipf.es web: http://bioinfo.cipf.es/dbau/ >>> >>> _______________________________________________ >>> IMP-users mailing list >>> IMP-users@salilab.org >>> https://salilab.org/mailman/listinfo/imp-users >> >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users