[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.
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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