ADL: Applying grid box for twisting protein

Diogo Martins diogo.stmart at gmail.com
Fri Apr 10 10:37:16 PDT 2020


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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