Hi, Siyu. The problem is that the ZDOCK file is not really a PDB file (see https://zlab.umassmed.edu/zdock/zdock_output_file.shtml for the ZDOCK output specification). The first few lines of your file look like:
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
while lines from PDB entry 1gcn looks like:
ATOM 1 N HIS A 1 49.668 24.248 10.436 1.00 25.00 N ATOM 2 CA HIS A 1 50.197 25.578 10.784 1.00 16.00 C
I guess Jmol and DS ViewerPro do not use the fields after the coordinates, but Chimera does. If you do not care about the extra fields, then the easiest approach is to remove columns 54 and on from the file. I used the command: awk '{printf("%54.54s\n", $0)}' < complex.1.pdb > c.1.pdb and c.1.pdb opened fine in Chimera. Of course, Chimera has a number of tools that can take advantage of non-coordinates information, e.g., render by attribute for custom coloring. If you want to incorporate the extra fields into the graphics, you may want to rewrite the file to cram some of them into the occupancy and temperature factor columns in the PDB file. Hope that helps. Conrad On 4/12/2016 7:33 PM, 赵思雨 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
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