Dear Hailiang, most maps (if not all) have the suggested contour level associated with them in the visualization tab of their EMDB entry. It is my understanding that this is the contour level that will account for the Van Der Waals volume of the protein. The Download tab allows you to download a CCP4-style map, which you can read in with your favorite molecular graphics package.
Filip Van Petegem On Thu, Jun 2, 2011 at 2:24 PM, Hailiang Zhang <[email protected]> wrote: > Hi, > > I am trying to compare a published EM map with X-ray map in hand, and have > several questions: > > 1. EM map seldom indicates the sigma level, and it was said because of the > box size uncertainty during EM model construction. Now, I wonder is there > any way we can sort of its equivalent sigma level to X-ray map? > > 2. The EM structure deposited in pdb don't have any experimental data, and > not sure how to obtain them and generate the map file. > > Sorry if this is wrong place to post EM questions. > > Hailiang > -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: [email protected] http://crg.ubc.ca/VanPetegem/
