Re: [PyMOL] problem saving the transformed coordinate after alignment

[Gabriel M. <gab...@sc...>]

Subha K,

You can just call cmd.save or save on the object name as so:

fetch 1oky 1t46, async=0
align 1oky, 1t46
save /tmp/1oky_transformed.pdb, 1oky

PyMOL will write out the transformed coordinates of 1oky into the pdb file. The structure of the alignment command is such that pymol transforms the first object onto the second.

align mobile, target

mobile will have it’s coordinates changed, target will be unchanged.

Regards,
Gabriel Marques
PyMOL


> On Oct 19, 2016, at 1:47 PM, Subha K <sub...@gm...> 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 <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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