[Chimera-users] Showbox

[Elaine Meng]

This page at the UCSF Dock website says to use dock_fans at googlegroups.com ... did you try that one?

<http://dock.compbio.ucsf.edu/Contact_Info/index.htm>

We (Chimera/X developers) are not the UCSF DOCK developers.  I personally worked on early versions of DOCK, but that was >25 years ago!!

I might have written that showbox thing a LONG time ago, but I've forgotten the details.  To the best of my memory, it is just to help in setting up the calculation of scoring grids.  The user (you) are the one who decides the scoring grid box size and location, and showbox is just for displaying a given box size and location so you can decide whether it is appropriate or not before calculating the grid.  Docking does not actually use that box.  If I remember correctly, the ligand could possibly fall outside of it, which just means that the ligand part outside the box will not contribute to its score.  Hopefully you would choose a grid box location that would enclose the spheres you want to use for docking, plus some additional space, so that most ligand poses would be fully inside of it.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 3, 2021, at 6:53 AM, Francesca Magarotto - francesca.magarotto2--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> I know that the program showbox is related to Dock, but I can't find a mailing list still active for Dock users...
> Maybe someone could help me here.
> I don't understand if ligands that are docked inside the binding site can exit in part from the box the user defines for grid calculation.
> I think that maybe if sphere centers are very near the boundaries of the box, it could be possible, but I'm not sure.
> Does anyone know it?
> Thanks and regards.