Tsjerk– You might be able to extract the ids of the aligned residues from an alignment object:
cmd.align(sele1,sele2copy,object="aln") [a.id for a in cmd.get_model('aln').atom] Since the alignment is sequential, I think this should contain all the aligned atoms from sele1 concatenated with the aligned atoms from sele2. However, as far as I know the internals of the alignment objects aren't documented, so I'm not sure if this can be relied upon. -Spencer On Tue, Oct 27, 2015 at 12:22 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Osvaldo, > > Probably that's the trick, although I'd need the indices, but that's > simple enough. > The 'equivalence' one is still standing though :) > > Thanks, > > Tsjerk > > On Tue, Oct 27, 2015 at 11:44 AM, Osvaldo Martin <aloctavo...@gmail.com> > wrote: > >> So, you want to know the best way to do this? >> >> Z = [at_x for at_x in X for at_y in Y if at_x.id == at_y.id] >> >> Or am I still not getting it right? >> >> Cheers, >> Osvaldo. >> >> On Tue, Oct 27, 2015 at 10:56 AM, Tsjerk Wassenaar <tsje...@gmail.com> >> wrote: >> >> Hi Osvaldo, >>> >>> I could have been more clear I guess. First of all, let's say I have >>> obtained the atom list of a selection: >>> >>> X = cmd.get_model(selection1).atom >>> >>> I'm doing stuff with that (PCA, to be exact), but now I want to display >>> the result only for a subselection. Probably getting the intersection of >>> the selections and then check which atoms there match with the original >>> selection is an approach. The question there is what the best way is for >>> checking identity of the atoms. >>> >>> The second issue is when there is no intersection of the selections, but >>> there may be correspondence, as in alignment. >>> >>> Thanks for thinking along, >>> >>> Tsjerk >>> >>> On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin <aloctavo...@gmail.com> >>> wrote: >>> >>>> Hi Tsjerk, >>>> >>>> Do you mean something like this? >>>> >>>> cmd.index("sel_1 and sel_2") >>>> >>>> I do not get the differences between your two cases. Whats the >>>> difference between “atoms which are both in selection 1 and 2” and >>>> “matching atoms in the two selections” >>>> >>>> Cheers, >>>> >>>> Osvaldo. >>>> >>>> On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar <tsje...@gmail.com> >>>> wrote: >>>> >>>> >>>>> Hi Thomas e.a., >>>>> >>>>> Given two selections, would there be an easy way to >>>>> >>>>> 1. find the atoms which are both in selection 1 and 2, and the indices >>>>> of those in the selections >>>>> >>>>> and >>>>> >>>>> 2. find the matching atoms in the two selections, like align does, and >>>>> the indices of those in the selections >>>>> >>>>> Thanks, >>>>> >>>>> Tsjerk >>>>> >>>>> -- >>>>> Tsjerk A. Wassenaar, Ph.D. >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> _______________________________________________ >>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: >>>>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>>>> >>>> >>>> >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >
------------------------------------------------------------------------------
_______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net