Re: [PyMOL] Common atoms in two selections (and their indices)

Hi Tsjerk, Spencer, Osvaldo, cmd.get_raw_alignment() might be what you are looking for. http://pymolwiki.org/index.php/Get_raw_alignment Cheers, Thomas On 27 Oct 2015, at 12:49, Spencer Bliven wrote: > Tsjerk– > > You might be able to extract the ids of the

Re: [PyMOL] Common atoms in two selections (and their indices)

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

Re: [PyMOL] Common atoms in two selections (and their indices)

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,

Re: [PyMOL] Common atoms in two selections (and their indices)

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 wrote: Hi Osvaldo, > > I could have been more clear I guess.

Re: [PyMOL] Common atoms in two selections (and their indices)

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 wrote: > So, you want to know the best way to do this? > >

Re: [PyMOL] Common atoms in two selections (and their indices)

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