On Feb 11, 2011, at 7:54 AM, Elisabeth Ortega wrote:

Hi all,

I'm trying to do a script to display the "best" rotamer of all the rotamers that the funcion getRotamers give to me. I use the function useRotamers to display them but now I only want to display the rotamer with the less number of clashes and the highest number of h- bonds. I know that getRotamers return to us a list with all the rotamers of an aminoacid sorted by probability but I don't have any idea about how display only one of the rotamers. Anyone know how I can do it?

It depends. If it's your code deciding which rotamer to use, you can call useRotamer with a list of "rotamers" that contains just the one rotamer you want. If you want Chimera to do the work of screening by number of h-bonds and clashes, use the useBestRotamers function. It's the function that implements the swapaa command. The arguments for the function are documented in the function itself. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu