Hi, Thank you for your answer. Sorry, I thought I attached an image to the e-mail, but it seemed to have disappeared. [cid:c9712065-eebd-40bb-8961-604771507890] 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@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
