Dears, I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX. Would it be possible? Best regards Jinxin
Hi Jinxin, Sorry, ChimeraX does not have a tool to run docking calculations. We currently recommend using the docking program directly (Autodock Vina, DOCK, or others), not from inside Chimera/ChimeraX. After you get the output docking results file, you can open and analyze it using Chimera's ViewDock tool or ChimeraX's ViewDockX tool. ViewDockX: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html> The Chimera tool "Autodock Vina" is not recommended for most research purposes anyway, because it does not allow very much sampling or searching a ligand database -- see the warning in the bottom part of the gray box on the help page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 Jul 11, 2022, at 2:29 AM, 刘 金鑫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dears, I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX. Would it be possible? Best regards Jinxin
Thanks, What a pity. I hope to add some simple functions, such as protein energy minimize. Best Regards, Jinxin Liu Wuxi AppTec Phone: +86-18811123206 WeChat: ljx_19901018 E-mail: liu_jinxin@wuxiapptec.com or jinxinliu90@icloud.com
在 2022年7月11日，22:50，Elaine Meng <meng@cgl.ucsf.edu> 写道：
Hi Jinxin, Sorry, ChimeraX does not have a tool to run docking calculations. We currently recommend using the docking program directly (Autodock Vina, DOCK, or others), not from inside Chimera/ChimeraX. After you get the output docking results file, you can open and analyze it using Chimera's ViewDock tool or ChimeraX's ViewDockX tool.
ViewDockX: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
The Chimera tool "Autodock Vina" is not recommended for most research purposes anyway, because it does not allow very much sampling or searching a ligand database -- see the warning in the bottom part of the gray box on the help page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 Jul 11, 2022, at 2:29 AM, 刘 金鑫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dears, I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX. Would it be possible? Best regards Jinxin
Although it's not the same as minimization, if the structure contains only standard residues (amino acids) and water, if you add hydrogens you can then do a little jiggling/relaxation using the "tug" command with zero force (unless you want to constrain any atoms to current positions) and low temperature. For example, to reduce clashes between nonhydrogen atoms: open 2gbp delete ligand addh display clashes ~H restrict both tug @ca to @ca force 0 temp 10 steps 100 frames 50 clashes ~H restrict both See tug: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> ...and clashes: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> For a more general minimization tool, including parametrization of nonstandard residues like ligands (which is not very simple), we are working on adding a procedure in ChimeraX similar to that in Chimera. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2022, at 8:02 AM, 刘 金鑫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks, What a pity. I hope to add some simple functions, such as protein energy minimize. Best Regards, Jinxin Liu Wuxi AppTec
Phone: +86-18811123206 WeChat: ljx_19901018 E-mail: liu_jinxin@wuxiapptec.com or jinxinliu90@icloud.com
在 2022年7月11日，22:50，Elaine Meng <meng@cgl.ucsf.edu> 写道：
Hi Jinxin, Sorry, ChimeraX does not have a tool to run docking calculations. We currently recommend using the docking program directly (Autodock Vina, DOCK, or others), not from inside Chimera/ChimeraX. After you get the output docking results file, you can open and analyze it using Chimera's ViewDock tool or ChimeraX's ViewDockX tool.
ViewDockX: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
The Chimera tool "Autodock Vina" is not recommended for most research purposes anyway, because it does not allow very much sampling or searching a ligand database -- see the warning in the bottom part of the gray box on the help page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 Jul 11, 2022, at 2:29 AM, 刘 金鑫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dears, I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX. Would it be possible? Best regards Jinxin
Thanks! 发自我的iPhone
在 2022年7月12日，00:58，Elaine Meng <meng@cgl.ucsf.edu> 写道：
Although it's not the same as minimization, if the structure contains only standard residues (amino acids) and water, if you add hydrogens you can then do a little jiggling/relaxation using the "tug" command with zero force (unless you want to constrain any atoms to current positions) and low temperature. For example, to reduce clashes between nonhydrogen atoms:
open 2gbp delete ligand addh display clashes ~H restrict both tug @ca to @ca force 0 temp 10 steps 100 frames 50 clashes ~H restrict both
See tug: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> ...and clashes: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
For a more general minimization tool, including parametrization of nonstandard residues like ligands (which is not very simple), we are working on adding a procedure in ChimeraX similar to that in Chimera.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2022, at 8:02 AM, 刘 金鑫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks, What a pity. I hope to add some simple functions, such as protein energy minimize. Best Regards, Jinxin Liu Wuxi AppTec
Phone: +86-18811123206 WeChat: ljx_19901018 E-mail: liu_jinxin@wuxiapptec.com or jinxinliu90@icloud.com
在 2022年7月11日，22:50，Elaine Meng <meng@cgl.ucsf.edu> 写道：
Hi Jinxin, Sorry, ChimeraX does not have a tool to run docking calculations. We currently recommend using the docking program directly (Autodock Vina, DOCK, or others), not from inside Chimera/ChimeraX. After you get the output docking results file, you can open and analyze it using Chimera's ViewDock tool or ChimeraX's ViewDockX tool.
ViewDockX: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
The Chimera tool "Autodock Vina" is not recommended for most research purposes anyway, because it does not allow very much sampling or searching a ligand database -- see the warning in the bottom part of the gray box on the help page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 Jul 11, 2022, at 2:29 AM, 刘 金鑫 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dears, I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX. Would it be possible? Best regards Jinxin
participants (2)
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Elaine Meng -
刘 金鑫