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 -- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
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