I think the answer is to just use save, not that save_transformed function.
-David
> On Oct 19, 2016, at 1:47 PM, Subha K <subhal...@gmail.com> wrote:
>
> Hi there,
>
> I am trying to save the transformed coordinates of an object after performing
> an alignment. I came across the save_transformed.py
> [https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but, this
> seems to give a completely different coordinate of the object and not the one
> that is aligned.
>
> Is there any other way of saving the coordinates of an object after
> performing an alignment?
>
> Thanks,
> Subha
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