[Chimera-users] PDB file created by a protein—protien docking tool ZDOCK can not opened by Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 13 12:21:16 PDT 2016


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 at 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>
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