I am running Chimera X. I downloaded autodock Vina. It should show as a tool>surface binding analysis but it is not there. How do I get the surface binding analysis option to show and to display Vina? Thanks. Michael
Hi Michael, ChimeraX does not have an interface to Autodock Vina. You must be looking at the Chimera User's Guide. UCSF Chimera and UCSF ChimeraX are two different programs; you would need to get Chimera to use this feature. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2023, at 6:37 PM, Michael Sacher via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I am running Chimera X. I downloaded autodock Vina. It should show as a tool>surface binding analysis but it is not there. How do I get the surface binding analysis option to show and to display Vina? Thanks. Michael
Thank you. That helped. One more issue. When I load the ligand, it is loading in the middle of the receptor. I am unable to move it away. I would like to select all of the receptor as a docking site but the ligand is being selected as well. How do I move the receptor or the ligand apart? Michael -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, December 21, 2023 10:33 PM To: Michael Sacher <michael.sacher@concordia.ca> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] autodock Vina Attention This email originates from outside the concordia.ca domain. // Ce courriel provient de l'extérieur du domaine de concordia.ca Hi Michael, ChimeraX does not have an interface to Autodock Vina. You must be looking at the Chimera User's Guide. UCSF Chimera and UCSF ChimeraX are two different programs; you would need to get Chimera to use this feature. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2023, at 6:37 PM, Michael Sacher via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I am running Chimera X. I downloaded autodock Vina. It should show as a tool>surface binding analysis but it is not there. How do I get the surface binding analysis option to show and to display Vina? Thanks. Michael
Hi Michael, Are we talking about ChimeraX or Chimera? In ChimeraX, here is how you move different models separately from each other (see the "selective manipulation" section at the bottom): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> In Chimera, here is how you move different models separately from each other (see "activation for motion"): <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> In the future, if you are asking about Chimera, please use the chimera-users@cgl.ucsf.edu address instead - thanks! Also it is best to include in the subject line the topic of your question. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 22, 2023, at 6:38 AM, Michael Sacher via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you. That helped. One more issue. When I load the ligand, it is loading in the middle of the receptor. I am unable to move it away. I would like to select all of the receptor as a docking site but the ligand is being selected as well. How do I move the receptor or the ligand apart? Michael
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, December 21, 2023 10:33 PM To: Michael Sacher <michael.sacher@concordia.ca> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] autodock Vina
Attention This email originates from outside the concordia.ca domain. // Ce courriel provient de l'extérieur du domaine de concordia.ca
Hi Michael, ChimeraX does not have an interface to Autodock Vina. You must be looking at the Chimera User's Guide.
UCSF Chimera and UCSF ChimeraX are two different programs; you would need to get Chimera to use this feature.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2023, at 6:37 PM, Michael Sacher via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I am running Chimera X. I downloaded autodock Vina. It should show as a tool>surface binding analysis but it is not there. How do I get the surface binding analysis option to show and to display Vina? Thanks. Michael
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participants (2)
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Elaine Meng -
Michael Sacher