Hi Yasser, It's not a bug. The RMSD between 2 atoms equals the distance. RMSD = root mean square distance, and if there is only one distance, the mean square distance is the same as the square distance, and then the root of that equals the distance. The rmsd command calculates RMSD without fitting. If you are trying to superimpose the atoms and then get an RMSD, you need to use the match command. Of course, the superposition will not be unique with only 2 atoms. Use the command "help rmsd" or "help match" to see the command manual pages. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 3, 2010, at 8:13 AM, Yasser Almeida Hernández wrote:

Hi all.... In Chimera , i selected a single pair of atoms for RMSD calculation with the command rms (rms #1:221.A@NE #0:221.A@NE) and it return the distance between the atoms ???? It would be a bug??? Please check this....