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? [cid:fc8bd8ab-4117-464a-b2fb-0f512e867f88] Thank you, Judith
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
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
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@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@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
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@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric, Thank you very much for taking the time to have a look at the SwissDock script. Thanks, Judith ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: 26 May 2020 21:39 To: Schaf, Judith (2017) <Judith.Schaf.2017@live.rhul.ac.uk> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Molecular docking 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@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Schaf, Judith (2017)