Hi Peter, Chimera does not do any threading (evaluating sequence compatibility with a 3D structure) or comparative modeling with energy evaluation. I am not sure what you mean by consensus structure, but there is nothing in Chimera currently that creates a new structure based on a set of input structures. In the future, we would like Chimera to interface with the separate program MODELLER for comparative modeling, but this has not been implemented. You can certainly align multiple input structures and get a corresponding sequence alignment, and you can add your sequence that doesn't have a structure to the sequence alignment and see where parts of it map onto the structures. If you want more details on any of these, let me know. 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 Mar 13, 2007, at 11:45 AM, Peter Murphy wrote:

Hi,

I have a quick question about your program. Normally (on a day to day basis) I use fairly basic features of chimera (coloring, etc) to produce pictures of crystal structure images (for presentations, papers, etc). Rarely do I have to use the more advanced features of chimera (Solvent accessible surface area, distance calculations, etc) so I don`t have a good idea of the limits of your program. Thus, I figured I would check to see if what I wanted to do is out of the scope of your program. I have a few crystal structures which I want to align (I now understand how to do this based on your online tutorial (thanks)), but what I really want to do is feed a third structure into the consensus structure (or if there is no consensus structure, just feed a known sequence into a known crystal structure to see if the sequence could form that structure.

Is there anyway to do this in your program..

Thanks for any help you may be able to provide,

-- Peter Murphy, B.Sc., M.Sc Candidate Atlantic Research Center Dalhousie University Halifax, Nova Scotia, Canada _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users