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<p class="MsoNormal">Hi Joe and David<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If you want to reduce the mesh density of a Chimera model before export, use the following two methods. These are much more elegant than mesh reduction after export, which can introduce errors. You can read our molecular 3D printing protocol
in JoVE for detailed instructions of model generation and printing:<o:p></o:p></p>
<p class="MsoNormal"><a href="https://www.jove.com/video/55427/3d-printing-of-biomolecular-models-for-research-and-pedagogy">https://www.jove.com/video/55427/3d-printing-of-biomolecular-models-for-research-and-pedagogy</a>
<o:p></o:p></p>
<p class="MsoNormal"><a href="https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.pdf">https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.pdf</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Ribbon models<o:p></o:p></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l1 level1 lfo3">Open Tools>depiction>ribbon style editor<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l1 level1 lfo3">Select the ‘cross section’ tab<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l1 level1 lfo3">Change the ribbon cross section to something simpler. You may draw a square, octagon or (a good balance) hexadecagon. Drawing the shapes can be a little tricky, but the results are
worth it!<o:p></o:p></li></ul>
<p class="MsoNormal"><o:p> </o:p></p>
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<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Surfaces<o:p></o:p></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l4 level1 lfo5">Instead of using the surface command from the menus, enter the following command in the command line” where ‘#0’ is the model number, and ‘0.5’ is the grid resolution in angstroms.
Higher grid values give less detailed meshes<o:p></o:p>
<ul style="margin-top:0in" type="circle">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l4 level2 lfo5">surf #0 grid 0.5<o:p></o:p></li></ul>
</li></ul>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">James Tyrwhitt-Drake<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Scientific Visualization Specialist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Contractor, Medical Science and Computing, Inc.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Bioinformatics and Computational Biosciences Branch (BCBB)
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">NIH/NIAID/OD/OSMO/OCICB<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Building 31, 3B62<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Bethesda, MD<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black">240-593-7508<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><a href="https://twitter.com/niaidbioit"><span style="color:#1F497D">@NIAIDBioIT</span></a> | <a href="https://twitter.com/nih3dprint"><span style="color:#1F497D">@NIH3Dprint</span></a></span><span style="font-size:10.5pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;color:#7F7F7F">Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient.
If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own
and not expressly made on behalf of the NIAID by one of its representatives.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Hurt, Darrell (NIH/NIAID) [E] <br>
<b>Sent:</b> Friday, September 22, 2017 6:48 AM<br>
<b>To:</b> Healey, Joe <J.R.J.Healey@warwick.ac.uk>; David Bhella <David.Bhella@glasgow.ac.uk><br>
<b>Cc:</b> NIH 3D Print Exchange <3Dprint@nih.gov><br>
<b>Subject:</b> Re: [Chimera-users] STL File export size<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Joe and David,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I encourage you to consider the NIH 3D Print Exchange (cc’d) as a place to easily create 3D-printable models of proteins of any size or complexity. We use Chimera as part of our toolchain, so the models will look familiar to you. Check
out the “Submit” function of the website to upload a PDB file and get a model in return. Or simply type in a PDB accession code for your model in the “Quick Submit” box to generate a model.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="https://3dprint.nih.gov">https://3dprint.nih.gov</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Full disclosure: I lead the team that maintains the Exchange.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Cheers,<o:p></o:p></p>
<p class="MsoNormal">Darrell<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt">Darrell Hurt, Ph.D.<br>
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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">"Healey, Joe" <<a href="mailto:J.R.J.Healey@warwick.ac.uk">J.R.J.Healey@warwick.ac.uk</a>><br>
<b>Date: </b>Friday, September 22, 2017 at 6:40 AM<br>
<b>To: </b>David Bhella <<a href="mailto:David.Bhella@glasgow.ac.uk">David.Bhella@glasgow.ac.uk</a>><br>
<b>Cc: </b>"<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
<b>Subject: </b>Re: [Chimera-users] STL File export size<o:p></o:p></span></p>
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<p><span style="font-size:12.0pt;color:black">Hi David,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Thanks very much! I'm currently experimenting with MeshMixer's "Reduce" to do the same kind of thing - though I think that will only get me so far. I'll certainly have a look at that walkthrough though.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">I have just realised part of my problem however, was that I was exporting the surface and ribbon representations though without realising it, rather than just the surface, which would be totally redundant when printed.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">Joe<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><u><span style="font-size:12.0pt;color:black"> </span></u><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">M.Sc. B.Sc. (Hons) MSRB</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">PhD Student</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">MOAC CDT, Senate House</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">University of Warwick</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">Coventry</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">CV47AL<br>
Mob: +44 (0) 7536 042620 | Email: <a href="mailto:J.R.J.Healey@warwick.ac.uk">J.R.J.Healey@warwick.ac.uk</a></span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">Jointly working in:</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/">Waterfield Lab</a> (<span style="background:white">WMS Microbiology and Infection
Unit)</span></span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/">Gibson Lab</a> (Warwick Chemistry)</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black">Twitter:
<a href="https://twitter.com/JRJHealey">@JRJHealey</a> | Website: </span><span style="font-size:12.0pt;color:black"><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey"><span style="font-size:10.0pt">MOAC Page</span></a> | ORCID: orcid.org/0000-0002-9569-6738<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> David Bhella <<a href="mailto:David.Bhella@glasgow.ac.uk">David.Bhella@glasgow.ac.uk</a>><br>
<b>Sent:</b> 22 September 2017 11:24:55<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
<b>Subject:</b> Re: [Chimera-users] STL File export size</span> <o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt">The free software package meshlab is very effective at reducing the complexity of 3D scenes for printing.<br>
There is a tutorial here:<br>
<a href="https://www.shapeways.com/tutorials/polygon_reduction_with_meshlab">https://www.shapeways.com/tutorials/polygon_reduction_with_meshlab</a><br>
<br>
<br>
D.<br>
<br>
Dr David Bhella<br>
Director - Scottish Macromolecular Imaging Centre<br>
<br>
MRC-University of Glasgow Centre for Virus Research<br>
Sir Michael Stoker Building<br>
Garscube Campus<br>
464 Bearsden Road<br>
Glasgow G61 1QH<br>
Scotland (UK)<br>
<br>
Telephone: 0141-330-3685<br>
Skype: d.bhella<br>
<br>
Virus structure group on Facebook: <a href="https://www.facebook.com/CVRstructure">
https://www.facebook.com/CVRstructure</a><br>
Molecular Machines - Images from Virus Research: <a href="http://www.molecularmachines.org.uk">
http://www.molecularmachines.org.uk</a><br>
<br>
CVR website: <a href="http://www.cvr.ac.uk">http://www.cvr.ac.uk</a><br>
CVR on Facebook: <a href="https://www.facebook.com/centreforvirusresearch">https://www.facebook.com/centreforvirusresearch</a>
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<br>
<br>
> On 22 Sep 2017, at 10:38, Healey, Joe <<a href="mailto:J.R.J.Healey@warwick.ac.uk">J.R.J.Healey@warwick.ac.uk</a>> wrote:<br>
> <br>
> Hi Chimera team,<br>
> <br>
> I'm dealing with some protein structures that vary quite a lot in size. I'd like to make 3D printable versions, so I'm exporting STL files.<br>
> <br>
> Is there any way to reduce the file size of the exported STLs? How might one control the level of detail (triangulation) of the exported file - I suspect the defaults are including a lot of detail that a 3D printer wouldn't even be able to replicate in the
first place.<br>
> <br>
> Many 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: <a href="mailto:J.R.J.Healey@warwick.ac.uk">
J.R.J.Healey@warwick.ac.uk</a><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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