Hi Johannes,
Did you read the PymoWIKI entry on the align command?
https://pymolwiki.org/index.php/Align#RMSD
I think this should give you what you want within PyMOL.
Btw, there is a nice dedicated PyMOL mailing list
https://pymolwiki.org/index.php/PyMOL_mailing_list
It is rather low traffic, but the replies are generally from the
developers or very knowledgeable users.
Hope this helps,
Folmer Fredslund
On 2017-08-27 13:09, Johannes Sommerkamp wrote:
> Hello everybody,
> I have superposed two structures based on the central beta-sheet CA
> atoms with the "super" command in Pymol.
> Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms
> without moving the structures again. The rms_cur command in Pymol
> would do that, but only works if all atom identifiers match. Adding
> "transform=0" to the super, oder align command still does the
> alignment and moves the structure but does not show the movement.
>
> Is there an easy way to just calculate the all atom RMSD between two
> already superposed structures in pymol or any other programm?
>
> Thanks in advance!
> Johannes
>
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