[chimerax-users] How to complete docking with ChimeraX

[刘 金鑫]

Thanks!

发自我的iPhone

> 在 2022年7月12日，00:58，Elaine Meng <meng at 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 at 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 at wuxiapptec.com or jinxinliu90 at icloud.com
>> 
>>>> 在 2022年7月11日，22:50，Elaine Meng <meng at 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 at 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
>>> 
>