Re: [chimerax-users] How to view SwissDock output in ViewDockX
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
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@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>
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@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@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>
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@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@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@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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participants (2)
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Eden Fussner - Dupas -
Elaine Meng