Hi Nevin, The sym command places molecule copies relative to the coordinate frame of a density map. If you do not have a density map open it will not work. The solution is to open a density map, any map will do even if it is not related to your system -- it is just providing a coordinate frame. Here's a density map (potassium ion channel electron microscope data) if you don't have one. ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1094/map/emd_1094.map.gz You'll need to uncompress it (for example, with gunzip, or on the Mac it will offer to uncompress automatically when you download it) before opening it in Chimera. Once it is open in Chimera and you use the sym command you can undisplay it with Favorites / Model Panel. You also use Model Panel to freeze the map (uncheck the "active" button) in order to make motions of the molecule generate new positions for the molecule copies. Here is why a map is needed to define a coordinate frame. You might think the positioning matrices could just be applied in the global coordinate frame. But when you rotate the Chimera models with the mouse to get a different view point, that moves all the models around in the global frame, and that would cause all the monomers to assume a new arrangement if the matrices were applied to the rotated reference model. So in order to be able to see you models from different view points without changing their relative positions the symmetries are applied relative to the coordinate frame of a density map. (Could be relative to any other model but the command was created for people fitting molecules into density maps.) If you rotate the density map and molecules together then the matrices still keep the same relative positions of the molecules. Tom Z. Nevin Gerek wrote:
Hello, I am having another problem with sym command. When I test on some proteins including the example (1i84) provided in the website, I get 'No opened volume or reference model specified" error. I used sym and then sym #0 but they give same error. Do I need to copy another feature for this command? Is there anyway I can fox this problem?
Thanks again,
Z. Nevin Gerek, Ph.D. Postdoctoral Fellow ----------------------------------------------------- The Center for Biological Physics Arizona State University PO Box 871504 Tempe, AZ 85287-1504 Phone: (480) 727-8897 nevin.gerek@asu.edu <mailto:nevin.gerek@asu.edu>