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Hi,</div>
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Thank you for your answer.</div>
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Sorry, I thought I attached an image to the e-mail, but it seemed to have disappeared.</div>
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<img size="19325" contenttype="image/png" unselectable="on" tabindex="-1" style="max-width: 100%; user-select: none;" data-outlook-trace="F:1|T:1" src="cid:c9712065-eebd-40bb-8961-604771507890"><br>
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When I say analyse I mean I submitt a docking on swissdock (<a href="http://www.swissdock.ch/" id="LPlnk330041">http://www.swissdock.ch/</a>) 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.</div>
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Judith</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 24 May 2020 20:54<br>
<b>To:</b> Schaf, Judith (2017) <Judith.Schaf.2017@live.rhul.ac.uk><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] Molecular docking</font>
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<div class="PlainText">Hi Judith,<br>
No idea -- to better ask the question, would have been helpful to attach an image and say what you mean by "analyse."
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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.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html</a>><br>
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Also if you selected something with Ctr-click or any of several other methods, then the selection is outlined in green.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html</a>><br>
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I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On May 24, 2020, at 10:18 AM, Schaf, Judith (2017) <Judith.Schaf.2017@live.rhul.ac.uk> wrote:<br>
> <br>
> Hi everybody,<br>
> <br>
> 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.<br>
> <br>
> Does someone know what this line represents? <br>
> <br>
> <br>
> <br>
> Thank you,<br>
> Judith<br>
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