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align moving, target, cycles=0, transform=0 align moving, target, cycles=0give identical values for RMSD. So, the only difference is, that the moving structure is not moved in the graphical output. Additionally the RMSD with the argument cycles=0 can't be the RMSD before any movement because the values differ for the super and the align command. I think its just without refinement.
[log in to unmask]">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
-- Johannes Sommerkamp Ruhr-Universität Bochum AG Röntgenstrukturanalyse an Proteinen, LS Biophysik, ND04/396 Universitätsstraße 150 44801 Bochum Tel: +49-(0)234/32-25754