Hi Chao Wu, The ordering is changed by the intersection (&) because the two sets of intersected atoms have different orders: in your case you wanted to keep the order in residue :1.het, but the set of all nonhydrogen atoms ( ~ element.H ) is in a different order. One way to do what you want is to delete the hydrogens before doing the RMSD calculation (be careful not to overwrite your original results files that includes the hydrogens, of course), for example: del :1.het & element.H (or maybe even just "del element.H" to delete all hydrogens) rmsd #0:1.het #1:1.het The disadvantage is that some other steps you do later might require the hydrogens, so you would have to close those files and open the original ones with hydrogens. If you don't delete the hydrogens, the only way I can think of is to specify all the atoms by name in the same order (brute force approach), for example: rmsd #0:1.het@c1@c2@c3@c4@c5@c6@o1@o2@o3@o4@o5@o6 #1:1.het@c1@c2@c3@c4@c5@c6@o1@o2@o3@o4@o5@o6 which can be hard to type and ugly. When I do something like that I usually text-edit to put it in a command file and then open the command file so I don't have to type it over and over. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Sep 27, 2008, at 7:04 AM, 吴超 wrote:

Hi, dear folks,

I want to evaluate the docking performance by calculating the RMSD of heavy atoms between ligand crystal conformation and docked conformation. I use the following command:

rmsd #0:1.het & ~element.H #1:1.het & ~element.H

But Chimera seems to forget the correct order and give a pairwise alignment not the way I want . I wonder if there is a way that I can get the correct selection order so as to calculate RMSD. Best

-- Chao Wu