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