i want to use CHIMERA software for superimposition of protein structure and find the RMSD ...if anyone know this procedure in chimera then tell me the steps.
First, load both structures for which you want to obtain RMSD value. Once uploaded they will appear as superimposed if they are similar to each other. Then click on Tools...Structure comparison...Matchmaker. In the window that appears, select one model in "reference structure" box and other in the "structure to match" box and click OK. In the bottom left corner of main window, you will see following line, "RMSD between.... atom pairs is....angstroms". Hope that helps
You just go in Chimera website there are video available for the same....its very simple.
First, load both structures for which you want to obtain RMSD value. Once uploaded they will appear as superimposed if they are similar to each other. Then click on Tools...Structure comparison...Matchmaker. In the window that appears, select one model in "reference structure" box and other in the "structure to match" box and click OK. In the bottom left corner of main window, you will see following line, "RMSD between.... atom pairs is....angstroms". Hope that helps
You can do this also on the RCSB PDB website: http://www.rcsb.org/pdb/workbench/workbench.do
- it is not Chimera, but you will get an RMSD in the end...
This gives the RMSD of all the atom pairs. Is it possible to get RMSD value for all the residues individually?
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