ViewDock

[tgarts97@…]

Hello,

I am using Chimerax for a school project and am required to input a pdb and
mol2 file. After opening the mol2 file, the viewdock interface is supposed
to automatically launch, however it does not for me. I have sent my files
to my professor to try on his end, and it does launch the viewdock
interface so there is no problem with the files, but rather the chimera
application. I am using the chimerax-daily.exe version, on my windows 11
pc. Please provide me any steps to troubleshoot this.

Thanks,
Ty

[Eric Pettersen]

Hi Ty,

About a month and a half ago the default behavior when opening Mol2 files was changed so that it only automatically shows the ViewDock tool if the Mol2 file contains multiple structures. If your file only contains one structure then that could explain why you and your professor get different behaviors. You can get the ViewDock tool to show with only one structure if you add "showTool true" to the command you are using to open the Mol2 file.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[tgarts97@…]

Hello,

Thanks for the response. How do I add that command to the tool im using to
open the mol2 file?

Ty

On Tue, Jun 16, 2026 at 12:13 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>
>
>

[Eric Pettersen]

You would have to open your Mol2 file using the ChimeraX command line, with the command
"open path-to-Mol2-file showTool true". Instead of typing out the full path to the Mol2 file, which might be tedious and error prone, there are a couple of shortcuts. One is to type "open browse showTool true" which will bring up a file browser for specifying the file. The other is to type "open ", then drag and drop the Mol2 file onto the command line from your system file browser -- which will fill in the path -- and then add " showTool true" to finish the command.

--Eric