Dears, Good night! I'm starting to use SwissDock to investigate new drugs. I'm having trouble viewing “the best result” through Chimera for Web (the browser cannot be configured) In the option “Download your predictions file” I can open all the ligands through ChimeraX (my computer's desktop) at the same time. But I would like to see only one ligand at a time. Would it be possible? Best regards Estela
Hi Estela, If you downloaded the ligand file, you don't need to configure your browser to use Chimera ViewDock. Just start Chimera and start Viewdock (in menu under Tools... Surface/Binding Analysis) and then in the resulting dialog, choose and open the downloaded ligand file. I don't remember what format Swissdock outputs, but I know Chimera ViewDock is commonly used for SwissDock results, so one of the format choices should work even though it doesn't say "swissdock": <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...> Since I can't remember what format Swissdock outputs, I can't say if the ViewDockX tool in ChimeraX would work with it, but you could try that too. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 20, 2020, at 8:05 AM, Estela Fernandes e Silva <star.fs@hotmail.com> wrote:
Dears, Good night! I'm starting to use SwissDock to investigate new drugs. I'm having trouble viewing “the best result” through Chimera for Web (the browser cannot be configured) In the option “Download your predictions file” I can open all the ligands through ChimeraX (my computer's desktop) at the same time. But I would like to see only one ligand at a time. Would it be possible? Best regards Estela
Dear Elaine, Thank you so much for your help! My Chimera was installed wrong, so I uninstalled and reinstalled a version compatible with my computer. Now I'm using Chimera perfectly. Thanks again Best regards Estela ________________________________ De: Elaine Meng <meng@cgl.ucsf.edu> Enviado: segunda-feira, 20 de abril de 2020 18:09 Para: Estela Fernandes e Silva <star.fs@hotmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Assunto: Re: [chimerax-users] Molecular Docking problem Hi Estela, If you downloaded the ligand file, you don't need to configure your browser to use Chimera ViewDock. Just start Chimera and start Viewdock (in menu under Tools... Surface/Binding Analysis) and then in the resulting dialog, choose and open the downloaded ligand file. I don't remember what format Swissdock outputs, but I know Chimera ViewDock is commonly used for SwissDock results, so one of the format choices should work even though it doesn't say "swissdock": <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h...> Since I can't remember what format Swissdock outputs, I can't say if the ViewDockX tool in ChimeraX would work with it, but you could try that too. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 20, 2020, at 8:05 AM, Estela Fernandes e Silva <star.fs@hotmail.com> wrote:
Dears, Good night! I'm starting to use SwissDock to investigate new drugs. I'm having trouble viewing “the best result” through Chimera for Web (the browser cannot be configured) In the option “Download your predictions file” I can open all the ligands through ChimeraX (my computer's desktop) at the same time. But I would like to see only one ligand at a time. Would it be possible? Best regards Estela
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Elaine Meng -
Estela Fernandes e Silva