[Chimera-users] Molecular docking

[Elaine Meng]

Hi Judith,
I don't know why the results file already has the green line shown, if you aren't doing anything in Chimera yourself to draw it.  Maybe you can ask the Swissdock server people.
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 25, 2020, at 1:22 AM, Schaf, Judith (2017) <Judith.Schaf.2017 at live.rhul.ac.uk> wrote:
> 
> Hi,
> Thank you for your answer.
> Sorry, I thought I attached an image to the e-mail, but it seemed to have disappeared.
> <image.png>
> 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.
> Judith
> 
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: 24 May 2020 20:54
> To: Schaf, Judith (2017) <Judith.Schaf.2017 at live.rhul.ac.uk>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at 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 at 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