PDB file created by a protein—protien docking tool ZDOCK can not opened by Chimera
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
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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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.html> 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>
Thanks for the assistance you have given me！ I have solved the problem. Best wishes！ -----原始邮件----- 发件人:"Elaine Meng" <meng@cgl.ucsf.edu> 发送时间:2016-04-14 03:21:16 (星期四) 收件人: "赵思雨" <154612254@csu.edu.cn> 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] PDB file created by a protein—protien docking tool ZDOCK can not opened by Chimera 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.html> 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
participants (3)
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Conrad Huang -
Elaine Meng -
赵思雨