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
