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:
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>>>>>
>>>> ​
>>>>
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> ​
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
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>
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