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

Conrad Huang conrad at cgl.ucsf.edu
Wed Apr 13 12:18:23 PDT 2016

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.


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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