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<p class="MsoNormal">Thank you Tom,</p>
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<p class="MsoNormal">Everything is working now perfectly.</p>
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<p class="MsoNormal">Best,</p>
<p class="MsoNormal">Artur</p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Artur BIELA, PhD</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Scientific Assistant</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Bionanoscience and Biochemistry Laboratory</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Malopolska Centre of Biotechnology</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:#222222">Jagiellonian University<br>
7A, Gronostajowa Street<br>
30-387 Krakow</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Poland</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black"> </span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Department of Cell Biology and Imaging</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Institute of Zoology and Biomedical Research</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Jagiellonian University</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">Gronostajowa 9</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">30-387 Krakow</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:black">artur.biela@uj.edu.pl</span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:#222222"><a href="http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory" target="_blank"><span style="color:#1155CC">http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory</span></a></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt; font-family:"Arial",sans-serif; color:#222222"><a href="https://publons.com/mashlets?el=badgeCont570&rid=M-3954-2019">publons</a></span></p>
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<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="border:none; padding:0cm"><b>Od: </b><a href="mailto:goddard@sonic.net">Tom Goddard</a><br>
<b>Wysłano: </b>czwartek, 5 września 2019 19:55<br>
<b>Do: </b><a href="mailto:artur.biela@uj.edu.pl">Artur Biela</a><br>
<b>DW: </b><a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
<b>Temat: </b>Re: [Chimera-users] cage builder</p>
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<div>Hi Artur,
<div class=""><br class="">
</div>
<div class=""> You can modify one line of the Cage Builder python code in your copy of Chimera to create buttons to make polygons with more sides. The file to modify is</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>chimera/share/CageBuilder/gui.py</div>
<div class=""><br class="">
</div>
<div class="">or on Mac</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Chimera.app/Contents/Resources/share/CageBuilder/gui.py</div>
<div class=""><br class="">
</div>
<div class="">and the line to modify is</div>
<div class=""><br class="">
</div>
<div class=""> apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,8)]</div>
<div class=""><br class="">
</div>
<div class="">which you could change replacing 8 by 16 to get</div>
<div class=""><br class="">
</div>
<div class=""> apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,16)]</div>
<div class=""><br class="">
</div>
<div class="">which would create buttons in the Cage Builder panel for polygons with 3 through 15 sides. After you edit the file with a text editor (keep the indentation of the line the same as this is important in Python), then restart Chimera and it will
have the new buttons.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Sep 5, 2019, at 1:10 AM, Artur Biela <<a href="mailto:artur.biela@uj.edu.pl" class="">artur.biela@uj.edu.pl</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
Hi all,</div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
</div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder.</div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
My question is: is there any option to use for example octagons, decagons or even more-gons?</div>
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</div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
Thank in advance</div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
Artur</div>
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</div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Artur BIELA, PhD</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Scientific Assistant</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Bionanoscience and Biochemistry Laboratory</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Malopolska Centre of Biotechnology</span></div>
</div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif; color:rgb(34,34,34)">Jagiellonian University<br class="">
7A, Gronostajowa Street<br class="">
30-387 Krakow</span></div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Poland</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif"> </span></div>
</div>
<div class="">
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Department of Cell Biology and Imaging</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Institute of Zoology and Biomedical Research</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Jagiellonian University</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">Gronostajowa 9</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">30-387 Krakow</span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif"> </span></div>
</div>
</div>
<div class="">
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif"><a href="mailto:artur.biela@uj.edu.pl" class="" style="color:blue; text-decoration:underline">artur.biela@uj.edu.pl</a></span></div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif; color:rgb(34,34,34)"><a href="http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory" target="_blank" class="" style="color:blue; text-decoration:underline"><span class="" style="color:rgb(17,85,204)">http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory</span></a></span></div>
</div>
</div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif; color:rgb(34,34,34)"><a href="https://publons.com/mashlets?el=badgeCont570&rid=M-3954-2019" class="" style="color:blue; text-decoration:underline">publons</a></span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; background-color:white">
<span class="" style="font-size:9.5pt; font-family:Arial,sans-serif">=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
</div>
</div>
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Chimera-users
mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline; font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">Chimera-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Manage
subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="" style="color:blue; text-decoration:underline; font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div>
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