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Thanks a lot for your answers and the PyMOL mailing list hint. I didnt had in mind this list. I read the Pymol Wiki. The commands align moving, target, cycles=0, transform=0 align moving, target, cycles=0 give 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. Since the two structure I want to compare are already aligned based on the central beta sheet CA atoms, I want to calculate the RMSD without any movement. Regards Johannes On 27/08/17 19:18, Folmer Fredslund wrote: > 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