Dear Yang, One issue is that you probably have single-layer transparency (default) where it shows only the top transparent layer. You can turn that off in the Effects tool, or with the command: ~set single That will allow one surface to show inside of the other, but not vice versa, because the second issue is that there are problems (bugs) with correctly rendering multiple transparent models. So instead of transparency of both surfaces, I recommend that you instead use mesh for one of the surfaces, since mesh is also see-through. 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 Jul 7, 2015, at 9:02 PM, 师扬 <sy31802@163.com> wrote:

Dear all, Recently, I have a task to display two EM density map ('A' and 'B') and one PDB ('C') at the same time. B and C fit in map to A. So, I need to make A and B transparent to observe them simultaneously. However, one strange thing happened when I made A and B transparent. I can only see the density which A is lager than B or B is larger than A, and I could not see the buried density. In another words, when I make both A and B transparent, the map can be changed in to the 'A+B' map, and I could not see any 'A-B' or 'B-A' information. Have anyone met this problem? Do change something in setting can solve this problem? Best regards Yang