[Chimera-users] I Can't Open My ZDOCK Output File Into Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 18 09:21:55 PDT 2017


Hi Nissa,
Well, the “.out” file is not PDB format or any format that Chimera knows about, and the rec[…]pdb and lig[…]pdb files are not really correct PDB format either.  They have some extra stuff after the X,Y,Z coordinates in each line that is different from the standard PDB format.  Maybe some other programs tolerate this extra stuff, but Chimera doesn’t.

See our “introduction to PDB format”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>

… and here’s a list of the kinds of docking outputs Chimera reads:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

So if you want to use Chimera to view the PDB files, you would have to edit them to delete the part of each ATOM line after the X,Y,Z coordinate values. I attach edited versions of your two files.  You could use whatever text-editing method you prefer.  

After you did that, you would be able to see the atomic structures, but Chimera still would not know how to read the ZDOCK “.out” file.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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> On Aug 18, 2017, at 12:20 AM, Nissa Nabila <nissanabilaabdulrazak at gmail.com> wrote:
> 
> And these as well, I missed to upload it earlier. Sorry for the inconvenient! :-(
> 
> On Fri, Aug 18, 2017 at 3:18 PM, Nissa Nabila <nissanabilaabdulrazak at gmail.com> wrote:
> Hello and hi! 
> 
> My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem?
> 
> Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review.
> 
> Thank you in advanced!
> 
> <lig.job122931.bl.pdb><rec.job122931.bl.pdb>


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