[cid:9962344b-5095-47ba-a1c2-1c6fef113ef2] Dear Official, I was unable to move the green grid, thus, I am unable to dock a compound on the protein target. Could you please help me with this? Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.
The Chimera help page explains how to move and resize the box with the mouse. See the "Receptor search volume options" and specifically the option to "Resize search volume using [button]": <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> If you have that option set to "button 2" then you would use mouse button 2 to move the box as in the description: "Dragging from a point not over the box translates the whole box in X and Y; Shift-dragging translates the box in the Z dimension." Or, you can just edit the Center and Size values in the Chimera Autodock Vina tool, but then it is harder to get the position you want compared to interactively moving it with the mouse. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2023, at 9:57 PM, Panapakam, Jyotheeswaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
<image.png> Dear Official, I was unable to move the green grid, thus, I am unable to dock a compound on the protein target. Could you please help me with this?
** Please also note that the Autodock Vina tool in Chimera is NOT recommended for most research purposes because the Chimera GUI settings only allow a very small amount of sampling. ** <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> For a more complete Autodock Vina calculation, you would need to run Autodock Vina directly (not using Chimera). See the Autodock Vina website: <https://vina.scripps.edu/>
On Jul 19, 2023, at 8:38 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
The Chimera help page explains how to move and resize the box with the mouse.
See the "Receptor search volume options" and specifically the option to "Resize search volume using [button]": <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
If you have that option set to "button 2" then you would use mouse button 2 to move the box as in the description:
"Dragging from a point not over the box translates the whole box in X and Y; Shift-dragging translates the box in the Z dimension."
Or, you can just edit the Center and Size values in the Chimera Autodock Vina tool, but then it is harder to get the position you want compared to interactively moving it with the mouse.
<Screen Shot 2023-07-19 at 8.32.43 AM.png>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2023, at 9:57 PM, Panapakam, Jyotheeswaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
<image.png> Dear Official, I was unable to move the green grid, thus, I am unable to dock a compound on the protein target. Could you please help me with this?
I tried everything, how ever things did not work out well. Is there anyway you can assist me over a zoom? Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas. ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 19 July 2023 10:38 AM To: Panapakam, Jyotheeswaran <JyotheeswaranPanapakam@my.unt.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: [EXT] Re: [Chimera-users] Unable to dock You don't often get email from meng@cgl.ucsf.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> The Chimera help page explains how to move and resize the box with the mouse. See the "Receptor search volume options" and specifically the option to "Resize search volume using [button]": <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> If you have that option set to "button 2" then you would use mouse button 2 to move the box as in the description: "Dragging from a point not over the box translates the whole box in X and Y; Shift-dragging translates the box in the Z dimension." Or, you can just edit the Center and Size values in the Chimera Autodock Vina tool, but then it is harder to get the position you want compared to interactively moving it with the mouse. [cid:82C0783D-BF4B-4F91-975E-49DC9377B85C] I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 18, 2023, at 9:57 PM, Panapakam, Jyotheeswaran via Chimera-users <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> wrote: <image.png> Dear Official, I was unable to move the green grid, thus, I am unable to dock a compound on the protein target. Could you please help me with this?
No, we do not offer that kind of support, sorry. Elaine
On Jul 19, 2023, at 7:20 PM, Panapakam, Jyotheeswaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
I tried everything, how ever things did not work out well. Is there anyway you can assist me over a zoom?
Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas. From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 19 July 2023 10:38 AM To: Panapakam, Jyotheeswaran <JyotheeswaranPanapakam@my.unt.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: [EXT] Re: [Chimera-users] Unable to dock
You don't often get email from meng@cgl.ucsf.edu. Learn why this is important The Chimera help page explains how to move and resize the box with the mouse.
See the "Receptor search volume options" and specifically the option to "Resize search volume using [button]": <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
If you have that option set to "button 2" then you would use mouse button 2 to move the box as in the description:
"Dragging from a point not over the box translates the whole box in X and Y; Shift-dragging translates the box in the Z dimension."
Or, you can just edit the Center and Size values in the Chimera Autodock Vina tool, but then it is harder to get the position you want compared to interactively moving it with the mouse.
<Screen Shot 2023-07-19 at 8.32.43 AM.png>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2023, at 9:57 PM, Panapakam, Jyotheeswaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
<image.png> Dear Official, I was unable to move the green grid, thus, I am unable to dock a compound on the protein target. Could you please help me with this?
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participants (2)
-
Elaine Meng -
Panapakam, Jyotheeswaran