When I say analyse I mean I submitt a docking on swissdock (http://www.swissdock.ch/) and then I download the results file and open it with chimera. There are always several potential binding sites, but only 1-3 have the green line between ligand and protein.

From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: 24 May 2020 20:54
To: Schaf, Judith (2017) <Judith.Schaf.2017@live.rhul.ac.uk>
Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Molecular docking

Hi Judith,
No idea -- to better ask the question, would have been helpful to attach an image and say what you mean by "analyse."

If you are finding H-bonds, for example, then the H-bonds might be shown with cyan lines between donors and acceptors, but if you chose to run such an analysis, I don't think the lines would be mysterious.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

Also if you selected something with Ctr-click or any of several other methods, then the selection is outlined in green.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

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

> On May 24, 2020, at 10:18 AM, Schaf, Judith (2017) <Judith.Schaf.2017@live.rhul.ac.uk> wrote:
>
> Hi everybody,
>
> I have a quick question: when I analyse the results of a molecular docking assay (performed with SwissDock) on Chimera I sometimes see a green line between the protein and the ligand.
>
> Does someone know what this line represents?
>
>
>
> Thank you,
> Judith