Dear Siyu Zhao, The file from ZDOCK does not follow the PDB format description because it has extra numbers in the wrong places after the X,Y,Z coordinates. Probably Jmol and DSV are not bothered by those extra numbers, but Chimera does not tolerate them. If you just remove the columns after the coordinates, the file will display in Chimera. Below I attached an edited copy of your file which includes only columns 1-54. ZDOCK output before editing: ATOM 1 N LYS A 2 -1.022 -5.354 37.251 4 1 1.63 -0.15 ATOM 2 CA LYS A 2 -1.230 -4.312 38.301 4 1 2.03 0.10 ATOM 3 C LYS A 2 0.011 -3.410 38.417 4 0 1.67 0.60 …after editing (OK for Chimera): ATOM 1 N LYS A 2 -1.022 -5.354 37.251 ATOM 2 CA LYS A 2 -1.230 -4.312 38.301 ATOM 3 C LYS A 2 0.011 -3.410 38.417 Example from RCSB PDB: ATOM 1 N ALA A 1 46.457 12.189 21.556 1.00 56.69 N ATOM 2 CA ALA A 1 47.614 11.997 22.448 1.00 55.96 C ATOM 3 C ALA A 1 47.538 12.947 23.645 1.00 55.17 C About PDB format: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.htm...> 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 12, 2016, at 7:33 PM, 赵思雨 <154612254@csu.edu.cn> wrote:
Excuse me： Thanks for your good tool.I'am a student studying bioinformatics.I have met a trouble.My PDB file created by a protein—protien docking tool ZDOCK.It can not opened by Chimera.But can opened by Jmol and DS ViewerPro Trial.While the graphic created by Chimera is more beautiful. One of the PDB file is in the accessory. Thanks Siyu Zhao <complex.1.pdb>