Re: [PyMOL] Atoms forming more bonds than they should have

[Wei S. <wei...@gm...>]

Hi Thomas,

This is a single docking poses produced by Autodock Vina. I did get several
poses, but all of them look similar and a flat structure. I am thinking of
that this might be due to the 2D (not 3D) structure of the lipid which I
used for protein docking as I was not able to get a 3D for this lipid. And
I am still trying to convert the 2D structure to a reliable 3D one.

Thanks,
Wei

On Tue, Jul 10, 2018 at 4:49 AM Thomas Holder <tho...@sc...>
wrote:

> Hi Wei,
>
> Is this an ensemble of docking poses all overlayed in the same PDB file,
> and not separated by MODEL records? PyMOL does distance based bonding when
> loading data from PDB files. Which docking program generated this file?
>
> Cheers,
>   Thomas
>
> > On Jul 9, 2018, at 4:57 PM, Wei Song <wei...@gm...> wrote:
> >
> > Hello,
> >
> > I got a structure (attached figure) of a lipid after docking it with a
> protein. The original structure before the docking is in SDF file, not
> regular PDB.   I've never seen a docked structure like this with many of
> the atoms having more bonds than they actually can have like some carbons
> (blue) are having five even six bonds in the display,  and the whole
> molecule looks like a plate.  Is there anyone who also have met this
> problem before or any idea to get the structure back normal display.
> >
> > Thank you and I appreciate any suggestions and ideas.
> >
> > Best,
> > Wei
> > <UNADJUSTEDNONRAW_thumb_f09.jpg>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>