Just use the "rms_cur" command instead of "align". https://pymolwiki.org/index.php/rms_cur
Cheers, Thomas > On Aug 28, 2017, at 10:04 AM, Johannes Sommerkamp > <0000155b9e78396e-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
