Hi Victor, I'll CC the chimera-users@cgl.ucsf.edu list -- that address is better for general Chimera "user" questions, while chimera-dev is more for "programmer" questions, i.e. involving python or other code. The "rmsd" command does not automatically use serial number to pair the atoms. You can control the order by specifying the residues and their atoms in the command. Of course, that can be painful if you want to include very many atoms in the calculation. If the order is not given in the command, "the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number" as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> You can see command manual pages using the "help" command, e.g.: help rmsd What approach is best depends on your particular case -- whether these are multi-residue macromolecules or single-residue small molecules, and how many atoms you want to include in the calculation. If they are single-residue small molecules, you might just modify the mol2 files so that the atoms you want to pair have the same names in the two structures (but unique within a structure). I hope this helps, 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 Jan 15, 2010, at 2:11 AM, Victor Muñoz wrote:
Hi, I want to calculate the RMSD between two mol2 structures in place. The two structures are different forms of the same structure. I haver modified the mol2 so that the two of them have the same serialNumber in their respective atoms. The problem is that when I use the command rmsd #model1 #model2, it return an incorrect value of the rmsd, as the value showed is too high, about 5, when it should be about 1 (the two structures are very similar). Is there any way to calculate the RMSD value in place correctly or I am doing anything wrong? Thanks for your help.