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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 >