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<p class="MsoNormal">Dear Eric,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you for the message. I am using version 1.3 (2021-12-08) for Mac. I have inspected the pdb and the endpoint atoms are all backbone atoms as far as I can see, so not sure what the problem is. There is by chance not a hidden maximum
distance or angle for pseudobonds to appear?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Wout<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Reply-To: </b>ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Date: </b>Friday, February 4, 2022 at 8:46 PM<br>
<b>To: </b>Wout Oosterheert <wout.oosterheert@mpi-dortmund.mpg.de><br>
<b>Cc: </b>"chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [chimerax-users] Pseudo bonds of missing structure in cartoon style<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Wout, <o:p></o:p></p>
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<p class="MsoNormal">What version of ChimeraX are you using? Also, for the problematic pseudobond are either of its endpoint atoms not peptide backbone atoms? If so, you will have to explicitly display the non-backbone atom in order for the pseudobond to
show (display of backbone atoms is "implied" by the cartoon depiction). Alternatively, you could delete the non-backbone atoms of the endpoint residue.<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"><o:p> </o:p></p>
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<p class="MsoNormal">Eric Pettersen<o:p></o:p></p>
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<p class="MsoNormal">UCSF Computer Graphics Lab<o:p></o:p></p>
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<p class="MsoNormal">On Feb 4, 2022, at 9:19 AM, Wout Oosterheert via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Dear ChimeraX team,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I’m making figures of a protein structure that has 4 residues missing in a flexible region. When I show the atoms as “style stick”, I can see a dashed pseudo bond between the two residues that connect the missing segment. However, when
I “show cartoons” of the same structure, the dashed line disappears and the pseudo bond is no longer visible. Would you have any suggestions on what to change to make the missing structure appear as a dashed line when the model is shown in cartoon style? <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Of interest, in a similar structure where 3 instead of 4 residues are missing, the dashed line is in fact shown when the model is shown in cartoon style. In addition, in regular Chimera the dashed line that represents the 4 missing residues
remains visible in cartoon style.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Thank you for your time.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal">Wout<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Wout Oosterheert, PhD<o:p></o:p></p>
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<p class="MsoNormal"><span style="border:none windowtext 1.0pt;padding:0in">Max Planck Institute of Molecular Physiology</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="DE" style="border:none windowtext 1.0pt;padding:0in">Otto-Hahn-Str. 11</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="DE" style="border:none windowtext 1.0pt;padding:0in">44227 Dortmund, Germany</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black;background:white">Phone +49-(0)231-133-2357</span><o:p></o:p></p>
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<p class="MsoNormal">Email:<span class="apple-converted-space"> </span><a href="mailto:wout.oosterheert@mpi-dortmund.mpg.de"><span style="color:#0563C1">wout.oosterheert@mpi-dortmund.mpg.de</span></a><o:p></o:p></p>
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<p class="MsoNormal"> <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 style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
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