Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you.
Best regards,
Luigi Marongiu Ph.D., B.Sc. (Hons.)
Dear Ute and Elaine,
I'm kind of saddened by this thread. Not only was the interface to Autodock vina useful for teaching, it is actually part of my workflow (with a few modifications), and it would be awesome with it could be implemented in chimeraX. The "small sampling problem" of the chimera interface is easily solvable. The maximum exhaustiveness allowed by the chimera interface is 8, a quick editing of the gui.py file, changing the max from 8 to 64 (line 25, for those interested) solves the problem (you have to delete the gui.pyc file so that the modified gui.py will be recompiled). MGLtools is aging and barelly runs on windows 11 and doesn't run at all on modern macs. The same can be said for Racoon. ChimeraX could be the de facto interface for autodock vina. If there really isn't any plans for implementing the vina interface, maybe I'll have to invest some time into creating a chimerax script/bundle, although a proper one created by the chimerax devs would be the ideal.
Hi Luigi, ChimeraX does not have an Autodock Vina interface (a tool to run Autodock Vina).
Although Chimera has an Autodock Vina interface, the Autodock Vina program is not part of Chimera. Instead this Chimera tool would send your data out to an Autodock Vina web service run by another group, and then get the results back and display them. That Autodock Vina web service is no longer available. With Chimera, however, you can still use its Autodock Vina interface if you also separately download Autodock Vina and install it on your own computer. However, even this is not recommended because the Chimera interface only allows a very small amount of sampling. For most scientific research, you should not use Chimera to run the docking, but just instead use Autodock Vina directly. This is explained in the Chimera help page for its Autodock Vina tool: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
After you get docking results from Autodock Vina, however, then you can view/analyze them using either Chimera (ViewDock tool) or ChimeraX (ViewDockX). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html https://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 Mar 12, 2023, at 1:04 AM, Luigi Marongiu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you.
Best regards,
Luigi Marongiu Ph.D., B.Sc. (Hons.)
Thank you Best regards Luigi ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Sunday, March 12, 2023 18:49 To: Luigi Marongiu luigi.marongiu@outlook.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Missing Vina on ChimeraX
Hi Luigi, ChimeraX does not have an Autodock Vina interface (a tool to run Autodock Vina).
Although Chimera has an Autodock Vina interface, the Autodock Vina program is not part of Chimera. Instead this Chimera tool would send your data out to an Autodock Vina web service run by another group, and then get the results back and display them. That Autodock Vina web service is no longer available. With Chimera, however, you can still use its Autodock Vina interface if you also separately download Autodock Vina and install it on your own computer. However, even this is not recommended because the Chimera interface only allows a very small amount of sampling. For most scientific research, you should not use Chimera to run the docking, but just instead use Autodock Vina directly. This is explained in the Chimera help page for its Autodock Vina tool: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
After you get docking results from Autodock Vina, however, then you can view/analyze them using either Chimera (ViewDock tool) or ChimeraX (ViewDockX). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html https://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 Mar 12, 2023, at 1:04 AM, Luigi Marongiu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you.
Best regards,
Luigi Marongiu Ph.D., B.Sc. (Hons.)
Dear Elaine,
thank you very much for your answer to this request. I understand that ChimeraX does not provide a direct interface to an AutoDock Vina web server.
However, the functionalities of the "AutoDock Vina" tool in Chimera (1. saving the receptor and the ligand pdbqt files, 2. defining the search volume, and 3. saving an AutoDock Vina input file) besides launching the docking were also immensely useful for us, especially for teaching purposes.
Would it be possible to provide these 3 functionalities also in ChimeraX, for example within the "Dock Prep" tool? The possibility to save a mol2 file is already provided, would it be possible to provide also the possibility to save pdbqt files for the receptor and the ligand?
Thank you in advance for your help. Ute
________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Luigi Marongiu via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Sunday, March 12, 2023 19:10 To: Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Missing Vina on ChimeraX
Thank you Best regards Luigi ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Sunday, March 12, 2023 18:49 To: Luigi Marongiu luigi.marongiu@outlook.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Missing Vina on ChimeraX
Hi Luigi, ChimeraX does not have an Autodock Vina interface (a tool to run Autodock Vina).
Although Chimera has an Autodock Vina interface, the Autodock Vina program is not part of Chimera. Instead this Chimera tool would send your data out to an Autodock Vina web service run by another group, and then get the results back and display them. That Autodock Vina web service is no longer available. With Chimera, however, you can still use its Autodock Vina interface if you also separately download Autodock Vina and install it on your own computer. However, even this is not recommended because the Chimera interface only allows a very small amount of sampling. For most scientific research, you should not use Chimera to run the docking, but just instead use Autodock Vina directly. This is explained in the Chimera help page for its Autodock Vina tool: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
After you get docking results from Autodock Vina, however, then you can view/analyze them using either Chimera (ViewDock tool) or ChimeraX (ViewDockX). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html https://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 Mar 12, 2023, at 1:04 AM, Luigi Marongiu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you.
Best regards,
Luigi Marongiu Ph.D., B.Sc. (Hons.)
Hello Ute, You may want to take a look at Raccoon and Raccoon2 from the AutoDock / AutoDock Vina developers:
https://autodock.scripps.edu/resources/raccoon/ https://autodock.scripps.edu/resources/raccoon2/
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2023, at 3:26 AM, Ute Roehrig via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
thank you very much for your answer to this request. I understand that ChimeraX does not provide a direct interface to an AutoDock Vina web server.
However, the functionalities of the "AutoDock Vina" tool in Chimera (1. saving the receptor and the ligand pdbqt files, 2. defining the search volume, and 3. saving an AutoDock Vina input file) besides launching the docking were also immensely useful for us, especially for teaching purposes.
Would it be possible to provide these 3 functionalities also in ChimeraX, for example within the "Dock Prep" tool? The possibility to save a mol2 file is already provided, would it be possible to provide also the possibility to save pdbqt files for the receptor and the ligand?
Thank you in advance for your help. Ute
From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Luigi Marongiu via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Sunday, March 12, 2023 19:10 To: Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Missing Vina on ChimeraX
Thank you Best regards Luigi From: Elaine Meng meng@cgl.ucsf.edu Sent: Sunday, March 12, 2023 18:49 To: Luigi Marongiu luigi.marongiu@outlook.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Missing Vina on ChimeraX
Hi Luigi, ChimeraX does not have an Autodock Vina interface (a tool to run Autodock Vina).
Although Chimera has an Autodock Vina interface, the Autodock Vina program is not part of Chimera. Instead this Chimera tool would send your data out to an Autodock Vina web service run by another group, and then get the results back and display them. That Autodock Vina web service is no longer available. With Chimera, however, you can still use its Autodock Vina interface if you also separately download Autodock Vina and install it on your own computer. However, even this is not recommended because the Chimera interface only allows a very small amount of sampling. For most scientific research, you should not use Chimera to run the docking, but just instead use Autodock Vina directly. This is explained in the Chimera help page for its Autodock Vina tool: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
After you get docking results from Autodock Vina, however, then you can view/analyze them using either Chimera (ViewDock tool) or ChimeraX (ViewDockX). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html https://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 Mar 12, 2023, at 1:04 AM, Luigi Marongiu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you.
Best regards,
Luigi Marongiu Ph.D., B.Sc. (Hons.)
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine,
thank you for this suggestion. Unfortunately, Raccoon does not run on modern Mac OS versions (Ventura, Monterey, Big Sur and Catalina), so it is not usable for teaching purposes.
Kind regards, Ute
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, March 13, 2023 17:11 To: Ute Roehrig Ute.Roehrig@sib.swiss Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Missing Vina on ChimeraX
Hello Ute, You may want to take a look at Raccoon and Raccoon2 from the AutoDock / AutoDock Vina developers:
https://autodock.scripps.edu/resources/raccoon/ https://autodock.scripps.edu/resources/raccoon2/
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2023, at 3:26 AM, Ute Roehrig via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
thank you very much for your answer to this request. I understand that ChimeraX does not provide a direct interface to an AutoDock Vina web server.
However, the functionalities of the "AutoDock Vina" tool in Chimera (1. saving the receptor and the ligand pdbqt files, 2. defining the search volume, and 3. saving an AutoDock Vina input file) besides launching the docking were also immensely useful for us, especially for teaching purposes.
Would it be possible to provide these 3 functionalities also in ChimeraX, for example within the "Dock Prep" tool? The possibility to save a mol2 file is already provided, would it be possible to provide also the possibility to save pdbqt files for the receptor and the ligand?
Thank you in advance for your help. Ute
From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Luigi Marongiu via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Sunday, March 12, 2023 19:10 To: Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Missing Vina on ChimeraX
Thank you Best regards Luigi From: Elaine Meng meng@cgl.ucsf.edu Sent: Sunday, March 12, 2023 18:49 To: Luigi Marongiu luigi.marongiu@outlook.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Missing Vina on ChimeraX
Hi Luigi, ChimeraX does not have an Autodock Vina interface (a tool to run Autodock Vina).
Although Chimera has an Autodock Vina interface, the Autodock Vina program is not part of Chimera. Instead this Chimera tool would send your data out to an Autodock Vina web service run by another group, and then get the results back and display them. That Autodock Vina web service is no longer available. With Chimera, however, you can still use its Autodock Vina interface if you also separately download Autodock Vina and install it on your own computer. However, even this is not recommended because the Chimera interface only allows a very small amount of sampling. For most scientific research, you should not use Chimera to run the docking, but just instead use Autodock Vina directly. This is explained in the Chimera help page for its Autodock Vina tool: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
After you get docking results from Autodock Vina, however, then you can view/analyze them using either Chimera (ViewDock tool) or ChimeraX (ViewDockX). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html https://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 Mar 12, 2023, at 1:04 AM, Luigi Marongiu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you.
Best regards,
Luigi Marongiu Ph.D., B.Sc. (Hons.)
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
carlos.emidio＠fisica.ufc.br -
Elaine Meng -
Luigi Marongiu -
Ute Roehrig