Specification of symmetry groups file for imp_sampcon --ambiguity option
Hi guys,
What is the specification of the symmetry groups file for imp_sampcon --ambiguity option?
Best, Jan
On 2/25/21 6:40 AM, Jan Kosinski wrote: > What is the specification of the symmetry groups file for imp_sampcon > --ambiguity option?
Looks like each line is just a list of equivalent subunits: https://github.com/salilab/imp-sampcon/blob/main/test/symminput/symm_groups....
Shruthi (who wrote this code) or Rakesh (who's used it recently IIRC) may have more information.
Ben
Hi Ben and all,
This actually just works for me, thanks for quick response!
And thanks Shruthi !
Best, Jan
> On 25. Feb 2021, at 19:44, Ben Webb ben@salilab.org wrote: > > On 2/25/21 6:40 AM, Jan Kosinski wrote: >> What is the specification of the symmetry groups file for imp_sampcon >> --ambiguity option? > > Looks like each line is just a list of equivalent subunits: > https://github.com/salilab/imp-sampcon/blob/main/test/symminput/symm_groups.... > > Shruthi (who wrote this code) or Rakesh (who's used it recently IIRC) may have more information. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
Ben is right. Each line is a symmetry group (list of proteins that should be considered equivalent for RMSD calculation). It should work for general cases. Let us know there's a problem.
Best Shruthi
On Fri, Feb 26, 2021 at 12:54 AM Jan Kosinski jan.kosinski@embl.de wrote:
> Hi Ben and all, > > This actually just works for me, thanks for quick response! > > And thanks Shruthi ! > > Best, > Jan > > > On 25. Feb 2021, at 19:44, Ben Webb ben@salilab.org wrote: > > > > On 2/25/21 6:40 AM, Jan Kosinski wrote: > >> What is the specification of the symmetry groups file for imp_sampcon > >> --ambiguity option? > > > > Looks like each line is just a list of equivalent subunits: > > > https://github.com/salilab/imp-sampcon/blob/main/test/symminput/symm_groups.... > > > > Shruthi (who wrote this code) or Rakesh (who's used it recently IIRC) > may have more information. > > > > Ben > > -- > > ben@salilab.org https://salilab.org/~ben/ > > "It is a capital mistake to theorize before one has data." > > - Sir Arthur Conan Doyle > > _______________________________________________ > > IMP-users mailing list > > IMP-users@salilab.org > > https://salilab.org/mailman/listinfo/imp-users > >
participants (3)
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Ben Webb -
Jan Kosinski -
Shruthi Viswanath