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<p>Hi Elaine,</p>
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<p>Ah you were quite right. I didn't realise from the docs that "preset" was literally the string itself, I thought it was indicating a variable portion of the name.</p>
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<p>Solved now!</p>
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<p>Thanks,</p>
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<p>Joe</p>
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Joe Healey<br style="font-size:10pt">
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons) MSRB</span><br>
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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 id="ms-rterangepaste-start"></span><span>orcid.org/0000-0002-9569-6738</span><span id="ms-rterangepaste-end"></span></div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 25 May 2017 16:59<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] custom presets not appearing</font>
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<div class="PlainText">Hi Joe,<br>
I think the issue is the script file name. As mentioned in the docs (see link in your message) it should be named something like Goodsell.preset.cmd<br>
<br>
Presumably you did the other steps: went to the Presets category in the Preferences (open from Favorites menu) and add the location of your personal preset directory, click Save.<br>
<br>
I guess logically we could use all the command and python files in the specified directory and not require the “preset” in the name, but currently it is required.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
<br>
> On May 25, 2017, at 1:29 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:<br>
> <br>
> Hi Chimera Team,<br>
> <br>
> 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.<br>
> <br>
> E.g, in /Users/joehealey/Documents/Warwick/PhD/Structural_Work/Scripts/Presets/<br>
> <br>
> I have the following script (chimera implemented one):<br>
> <br>
> # Goodsell.cmd<br>
> <br>
> #############################################################<br>
> # #<br>
> # Chimera syntax commands for use as a preset. Sets the <br>
> #<br>
> # depiction in the style of David Goodsell.<br>
> #<br>
> # (The PDB Molecule-of-the-Month style).<br>
> #<br>
> # #<br>
> #############################################################<br>
> <br>
> # Create lower resolution surface models:<br>
> sym surfaces all resolution 2<br>
> <br>
> # Hide dashed bonds that may appear though the surface<br>
> setattr g display false<br>
> <br>
> # Apply silhouette edging and colouring<br>
> set silhouetteWidth 3.5<br>
> set silhouetteColor black<br>
> set silhouette<br>
> <br>
> # Set depth cueing depth and colour<br>
> <br>
> set dcColor black<br>
> set dcStart 0.5<br>
> set dcEnd 1.5<br>
> <br>
> # Set background transparency<br>
> set bgTransparency<br>
> <br>
> # Set lighting mode for flat rendering<br>
> lighting mode ambient<br>
> <br>
> # Hide ribbons<br>
> ~ribbon<br>
> <br>
> # Set surface colour<br>
> color red ,s<br>
> <br>
> # Make sure molecule is in focus<br>
> focus<br>
> <br>
> However, as per the documentation ( <a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets">
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets</a> ) the preset doesn't appear in the presets menu.<br>
> <br>
> 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?<br>
> <br>
> I suspect I'm missing something?<br>
> <br>
> Thanks,<br>
> <br>
> Joe Healey<br>
> <br>
> <br>
> M.Sc. B.Sc. (Hons) MSRB<br>
> PhD Student<br>
> MOAC CDT, Senate House<br>
> University of Warwick<br>
> Coventry<br>
> CV47AL<br>
> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk<br>
> <br>
> Jointly working in:<br>
> Waterfield Lab (WMS Microbiology and Infection Unit)<br>
> and the Gibson Lab (Warwick Chemistry)<br>
> <br>
> Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738<br>
> _______________________________________________<br>
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<br>
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