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Hi Eric,</div>
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Thank you very much for taking the time to have a look at the SwissDock script.</div>
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Thanks,</div>
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Judith </div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> 26 May 2020 21:39<br>
<b>To:</b> Schaf, Judith (2017) <Judith.Schaf.2017@live.rhul.ac.uk><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] Molecular docking</font>
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<div class="PlainText">I just discovered that script that Swissdock uses to show its results displays hydrogen bonds as green lines.<br>
<br>
--Eric<br>
<br>
Eric Pettersen<br>
UCSF Computer Graphics Lab<br>
<br>
<br>
> On May 25, 2020, at 9:00 AM, Elaine Meng <meng@cgl.ucsf.EDU> wrote:<br>
> <br>
> Hi Judith,<br>
> 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.<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>
> <br>
>> On May 25, 2020, at 1:22 AM, Schaf, Judith (2017) <Judith.Schaf.2017@live.rhul.ac.uk> wrote:<br>
>> <br>
>> Hi,<br>
>> Thank you for your answer.<br>
>> Sorry, I thought I attached an image to the e-mail, but it seemed to have disappeared.<br>
>> <image.png><br>
>> When I say analyse I mean I submitt a docking on swissdock (<a href="http://www.swissdock.ch/">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.<br>
>> Judith<br>
>> <br>
>> From: Elaine Meng <meng@cgl.ucsf.edu><br>
>> Sent: 24 May 2020 20:54<br>
>> To: Schaf, Judith (2017) <Judith.Schaf.2017@live.rhul.ac.uk><br>
>> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
>> Subject: Re: [Chimera-users] Molecular docking<br>
>> <br>
>> 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."
<br>
>> <br>
>> 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>
>> <br>
>> 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>
>> <br>
>> 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>
>>> 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>
>>> Does someone know what this line represents? <br>
>>> Thank you,<br>
>>> Judith<br>
> <br>
> <br>
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