[Chimera-users] Molecular docking

[Eric Pettersen]

I just discovered that script that Swissdock uses to show its results displays hydrogen bonds as green lines.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On May 25, 2020, at 9:00 AM, Elaine Meng <meng at cgl.ucsf.EDU> wrote:
> 
> 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
> 
> 
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