I know what RMSD value is but i often encounter RMS in pymol as well as in certain docking programs. I tried to search the term online but didn't find any satisfying answer.
The RMSD is just the deviation of RMS of one structure component to the other on superimposition so on PyMol you may often encounter RMS for your atoms on a single structure rather than a superimposed RMSD.
RMSD=====RMS
http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/
I have superimposed two ligands in Schrodinger to show there is not similarity in their structure. The RMS was 0.1355. How should I explain this?
Look in details at which atoms were superimposed on which - I would suspect that only a small subset were used, e.g. just one aromatic ring or something similar.
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