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 <spencer.bli...@gmail.com> wrote: > 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. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ _______________________________________________ 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
