Hi, Please see this information on “saving maps after fitting” (near the bottom of the page): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> Basically you need to resample the fitted map on the grid of the other map. The link above gives more details. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 27, 2016, at 9:11 AM, 许靖蔚 <xujw13@mails.tsinghua.edu.cn> wrote:

Dear all: I recently have to match two maps and calculate the CC value between them. The origin of these two maps are different and the pixel value are also not the same. I could open these two maps in chimera and align them by map fitting. However, after I matched one of them to the other and saved the map, the re-opened map was still at the same position as the previous! So do you know how to same the map after fitting?

Best wishes.