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

[Nissa Nabila]

Alright, thank you for your responses. Have a nice day ahead! :-)

On Sat, Aug 19, 2017 at 12:21 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
>
>
>
> > 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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