May be you should try pdbefold server. It provides rmsd between equivalent CA atoms of superimposed structures.
All the best. Vipul Panchal, Ph.D. student CSIR-IGIB (M)- 091 7678617949 On 27-Aug-2017 4:50 PM, "Johannes Sommerkamp" < 0000155b9e78396e-dmarc-requ...@jiscmail.ac.uk> 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 >
