ADL: Autodock/Vina plugin and python version ; was: Re: Applying grid box for twisting protein

Jorge Iulek iulek at
Fri Apr 10 11:06:06 PDT 2020

Dear Diogo,

         To get into the thread, to my humble knowledge this plugin 
works within python 2.7, is there a workaround when pymol runs under 
python 3.6?


> The box can't be rotated, but the protein can. In Pymol, you can change the
> mouse mode to "3-button-editing" at the bottom right corner of the Pymol
> window, and use shift+left click to rotate your protein. Then you can save
> the new coordinates (File->Save Molecule). There's an Autodock/Vina plugin
> to show a grid box.
> On Fri, 10 Apr 2020 at 10:01, Leo Juhlin <leojuhlin at> wrote:
>> I have a twisting protein that I want to dock a molecule on. However, as
>> you can see in the picture below, the applied grid box is not parallel to
>> the leaning protein, which means that I have to make the grid box a lot
>> bigger in order to fit the residues between the twisting chains. Is there
>> any way to adjust the grid box or the protein so that they are aligned?
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