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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Fantastic, Eric!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Eric Pettersen [mailto:pett@cgl.ucsf.edu]
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<b>Sent:</b> Friday, January 13, 2017 5:39 PM<br>
<b>To:</b> Markus Heller<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] Preference/default for H-bond representation<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Markus,<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>I’ll make sure to include it in the ChimeraX implementation when I get there. To get ChimeraX where it needs to go I can’t put too much work into the current Chimera but nonetheless I added
a “lineType” option to the hbonds/findhbonds command so that at least in the command version you can get dashed H-bonds without code modifications. The valid options for the lineType are: solid, dashed, dotted, dash-dot, and dash-dot-dot. The option will
be available in the next daily build.<o:p></o:p></p>
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<p class="MsoNormal">—Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="color:black">
</span></span><span style="color:black">Eric Pettersen<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="color:black">
</span></span><span style="color:black">UCSF Computer Graphics Lab<o:p></o:p></span></p>
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<p class="MsoNormal">On Jan 12, 2017, at 1:55 PM, Markus Heller <<a href="mailto:mheller@cdrd.ca">mheller@cdrd.ca</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Great Eric, thanks. Works as advertised.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Any chance of making this more straightforward in ChimeraX or future Chimera releases?</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span class="apple-converted-space"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span></span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Eric
Pettersen [<a href="mailto:pett@cgl.ucsf.edu">mailto:pett@cgl.ucsf.edu</a>]<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Thursday, January 12, 2017 12:47 PM<br>
<b>To:</b><span class="apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB<br>
<b>Cc:</b><span class="apple-converted-space"> </span>Markus Heller<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [Chimera-users] Preference/default for H-bond representation</span><o:p></o:p></p>
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<p class="MsoNormal">On Jan 12, 2017, at 12:28 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu"><span style="color:purple">meng@cgl.ucsf.edu</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">There must be some place in the code to change it to always dashed, but somebody else would have to advise on that…</span><o:p></o:p></p>
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<p class="MsoNormal">To have all hydrogen bonds start out dashed, after line 991 of <your Chimera>/share/FindHBond/base.py (which should be “pbg.lineWidth = lineWidth”) add:<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>pbg.lineType = chimera.Dash<o:p></o:p></p>
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<p class="MsoNormal">with the same indentation as the preceding line. On a Mac, “<your Chimera>” will be Chimera.app/Contents/Resources.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">—Eric<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>Eric Pettersen<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>UCSF Computer Graphics Lab<o:p></o:p></p>
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