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

Diogo Martins diogo.stmart at gmail.com
Fri Apr 10 12:17:01 PDT 2020


Hello, unfortunately I don't know of any workaround.


On Fri, 10 Apr 2020 at 11:18, Jorge Iulek <iulek at uepg.br> wrote:

> 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?
>
>
> J.
>
>
> > 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 gmail.com> 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?
> >>
> >>
> >> https://imgur.com/a/qISzPKI
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> >>
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> >
> >
>
>
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