Hi Joe and David

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:

https://www.jove.com/video/55427/3d-printing-of-biomolecular-models-for-research-and-pedagogy

https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.pdf

Ribbon models

Open Tools>depiction>ribbon style editor
Select the ‘cross section’ tab
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!

Surfaces

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
- surf #0 grid 0.5

Regards,

James Tyrwhitt-Drake

Scientific Visualization Specialist

Contractor, Medical Science and Computing, Inc.

Bioinformatics and Computational Biosciences Branch (BCBB)

NIH/NIAID/OD/OSMO/OCICB

Building 31, 3B62

Bethesda, MD

240-593-7508

@NIAIDBioIT | @NIH3Dprint

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From: Hurt, Darrell (NIH/NIAID) [E]
Sent: Friday, September 22, 2017 6:48 AM
To: Healey, Joe <J.R.J.Healey@warwick.ac.uk>; David Bhella <David.Bhella@glasgow.ac.uk>
Cc: NIH 3D Print Exchange <3Dprint@nih.gov>
Subject: Re: [Chimera-users] STL File export size

Hi Joe and David,

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.

https://3dprint.nih.gov

Full disclosure: I lead the team that maintains the Exchange.

Cheers,

Darrell

Darrell Hurt, Ph.D.
Chief, Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, 4A50
North Bethesda, MD 20852

Office: 240-669-2741

Mobile: 301-758-3559

Web: BCBB Home Page
Twitter: @niaidbioit , @NIH3Dprint

From: "Healey, Joe" <J.R.J.Healey@warwick.ac.uk>
Date: Friday, September 22, 2017 at 6:40 AM
To: David Bhella <David.Bhella@glasgow.ac.uk>
Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] STL File export size

Hi David,

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.

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.

Joe

M.Sc. B.Sc. (Hons) MSRB

PhD Student

MOAC CDT, Senate House

University of Warwick

Coventry

CV47AL
Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk

Jointly working in:

Waterfield Lab (WMS Microbiology and Infection Unit)

and the Gibson Lab (Warwick Chemistry)

Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738

From: David Bhella <David.Bhella@glasgow.ac.uk>
Sent: 22 September 2017 11:24:55
To: Healey, Joe
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] STL File export size

The free software package meshlab is very effective at reducing the complexity of 3D scenes for printing.
There is a tutorial here:
https://www.shapeways.com/tutorials/polygon_reduction_with_meshlab

D.

Dr David Bhella
Director - Scottish Macromolecular Imaging Centre

MRC-University of Glasgow Centre for Virus Research
Sir Michael Stoker Building
Garscube Campus
464 Bearsden Road
Glasgow G61 1QH
Scotland (UK)

Telephone: 0141-330-3685
Skype: d.bhella

Virus structure group on Facebook: https://www.facebook.com/CVRstructure
Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk

CVR website: http://www.cvr.ac.uk
CVR on Facebook: https://www.facebook.com/centreforvirusresearch

> On 22 Sep 2017, at 10:38, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:
>
> Hi Chimera team,
>
> 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.
>
> 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.
>
> Many thanks
>
> Joe Healey
>
>
> M.Sc. B.Sc. (Hons) MSRB
> PhD Student
> MOAC CDT, Senate House
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk
>
> Jointly working in:
> Waterfield Lab (WMS Microbiology and Infection Unit)
> and the Gibson Lab (Warwick Chemistry)
>
> Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738
> _______________________________________________
> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users