[chimerax-users] How to view SwissDock output in ViewDockX

[Elaine Meng]

Thanks!

I don't have direct experience, but I know many people use Chimera for viewing SwissDock output, and there are videos for using SwissDock + Chimera :

<https://www.youtube.com/watch?v=KcZ1EV_FcK8>
<https://www.youtube.com/watch?v=CxHaAnI-LDQ>

Best,
Elaine

> On Feb 27, 2022, at 8:49 AM, Eden Fussner - Dupas via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Oh thank you so much Elaine - so if I just switch to the original Chimera it will work… thank you!
> 
> Yes, please go ahead. If it’s helpful for others using SwissDock and Chimera - fine with me.
> 
> Cheers,
> Eden
> 
> 
> 
>> On Feb 27, 2022, at 11:41 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Sorry, as mentioned in this previous post, ChimeraX does not yet support reading SwissDock output into ViewDockX:
>> 
>> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-February/001909.html>
>> 
>> There is a ticket about this in the ChimeraX bug/request database, and I'll add you to the list of people to notify if there are updates on this issue:
>> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4232>
>> 
>> Would it be OK to add your sample data to this ticket (the database is publicly available)?
>> 
>> For now, you would need to keep using Chimera ViewDock for SwissDock results.
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Feb 26, 2022, at 4:20 PM, Eden Fussner - Dupas via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Elaine,
>>> 
>>> I’m not sure if you’ve answered this elsewhere - but I am having the same issue another user was having. The output of Swissdock isn’t being recognized by the ViewDockX tool.
>>> 
>>> I am trying to pick the best model stearic acid in this PLAT protein (an AlphaFold model). Any help would be most appreciated.
>>> 
>>> Warmly,
>>> Eden
>>> 
>>> <target.pdb><clusters.dock4.pdb>
> 
> 
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