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<p>Hi Chimera Team,</p>
<p><br>
</p>
<p>I've defined a custom preset (implemented in both python and 'chimera language'), and I've placed in a folder which I have directed the custom preset dialogue to.</p>
<p><br>
</p>
<p>E.g, in <span>/Users/joehealey/Documents/Warwick/PhD/Structural_Work/Scripts/Presets/</span></p>
<p><span><br>
</span></p>
<p><span>I have the following script (chimera implemented one):</span></p>
<p><span><br>
</span></p>
<p><span></p>
<div># Goodsell.cmd</div>
<div><br>
</div>
<div>#############################################################</div>
<div>#<span class="Apple-tab-span" style="white-space:pre"> </span>#</div>
<div># Chimera syntax commands for use as a preset. Sets the <span class="Apple-tab-span" style="white-space:pre">
</span>#</div>
<div># depiction in the style of David Goodsell.<span class="Apple-tab-span" style="white-space:pre">
</span>#</div>
<div># (The PDB Molecule-of-the-Month style).<span class="Apple-tab-span" style="white-space:pre">
</span>#</div>
<div>#<span class="Apple-tab-span" style="white-space:pre"> </span>#</div>
<div>#############################################################</div>
<div><br>
</div>
<div># Create lower resolution surface models:</div>
<div>sym surfaces all resolution 2</div>
<div><br>
</div>
<div># Hide dashed bonds that may appear though the surface</div>
<div>setattr g display false</div>
<div><br>
</div>
<div># Apply silhouette edging and colouring</div>
<div>set silhouetteWidth 3.5</div>
<div>set silhouetteColor black</div>
<div>set silhouette</div>
<div><br>
</div>
<div># Set depth cueing depth and colour</div>
<div><br>
</div>
<div>set dcColor black</div>
<div>set dcStart 0.5</div>
<div>set dcEnd 1.5</div>
<div><br>
</div>
<div># Set background transparency</div>
<div>set bgTransparency</div>
<div><br>
</div>
<div># Set lighting mode for flat rendering</div>
<div>lighting mode ambient</div>
<div><br>
</div>
<div># Hide ribbons</div>
<div>~ribbon</div>
<div><br>
</div>
<div># Set surface colour</div>
<div>color red ,s</div>
<div><br>
</div>
<div># Make sure molecule is in focus</div>
<div>focus</div>
<br>
</span>
<p></p>
<p>However, as per the documentation ( <a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets" class="OWAAutoLink" id="LPlnk327960" previewremoved="true">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets</a> )
the preset doesn't appear in the presets menu.</p>
<p><br>
</p>
<p>I can execute the script as normal with exec, and it works and has the desired effect, but I'd like it to be in the preset menu if possible?</p>
<div><br>
</div>
I suspect I'm missing something?
<div><br>
</div>
<div>Thanks,<br>
<p><br>
</p>
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Joe Healey<br style="font-size:10pt">
</div>
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<br>
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<span style="text-decoration:underline"> </span><br>
</div>
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons) MSRB</span><br>
</div>
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<span style="font-size:10pt"></span>
<div><span style="font-size:10pt">PhD Student</span></div>
<div><span style="font-size:10pt">MOAC CDT, Senate House</span></div>
<div><span style="font-size:10pt">University of Warwick<br style="">
</span></div>
<div><span style="font-size:10pt">Coventry<br style="">
</span></div>
<div><span style="font-size:10pt">CV47AL<br style="">
Mob: +44 (0) 7536 042620 | </span><span style="font-size:10pt">Email: J.R.J.Healey@warwick.ac.uk</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Jointly working in:<br style="">
</span></div>
<div><span style="font-size:10pt"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP">Waterfield Lab</a> (<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">WMS </span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Microbiology
and Infecti</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">on Un</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">it)</span></span></div>
<div><span style="font-size:10pt">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP">Gibson Lab</a> (Warwick Chemistry)<br style="">
</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Twitter: <a href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a> | </span><span style="font-size:10pt">Website: </span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="font-size:10pt" id="LPNoLP">MOAC Page</a> | ORCID: <span>orcid.org/0000-0002-9569-6738</span></div>
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