[Chimera-users] STL File export size

Fri Sep 22 07:36:32 PDT 2017

Hi Joe,

For very large structures such as viruses we use the sym command instead of the grid command.  First we try "sym #0 surfaces all resolution 4 " and if that doesn't work (too large) we try "sym #0 surfaces all resolution 8"

For regular surfaces we define the gridsize as lognumAtoms - 2.5

The largest grid size we use is 2.5.  You will need to experiment to find what works for your structure.  Start low resolution and go higher!

You can look through our pipeline script to see exactly which commands we give Chimera to generate models: https://github.com/niaid/3Dmodel_scripts/blob/master/Chimera_Molecular.py

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<https://twitter.com/niaidbioit> | @NIH3Dprint<https://twitter.com/nih3dprint>

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.

From: Healey, Joe [mailto:J.R.J.Healey at warwick.ac.uk]
Sent: Friday, September 22, 2017 10:11 AM
To: Tyrwhitt-Drake, James (NIH/NIAID) [C] <james.tyrwhitt-drake at nih.gov>; Hurt, Darrell (NIH/NIAID) [E] <darrellh at niaid.nih.gov>; David Bhella <David.Bhella at glasgow.ac.uk>
Cc: NIH 3D Print Exchange <3Dprint at nih.gov>; chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] STL File export size

Hi James,

That's a great little resource, thanks very much! The structures I'm dealing with don't play nicely with the default surface parameters, so the grid size has done wonders.

Out of interest, what sort of size would you consider reasonable for printing of a large viral assembly if you were doing the printing? The models currently have about a million and a half atoms, and the STL files are coming out at a few GB at present (hence me wanting to optimise the shrinking and remeshing).

Thanks,

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 at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
________________________________
From: Tyrwhitt-Drake, James (NIH/NIAID) [C] <james.tyrwhitt-drake at nih.gov<mailto:james.tyrwhitt-drake at nih.gov>>
Sent: 22 September 2017 14:33:23
To: Hurt, Darrell (NIH/NIAID) [E]; Healey, Joe; David Bhella
Cc: NIH 3D Print Exchange; chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>
Subject: RE: [Chimera-users] STL File export size

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!

[X]

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<https://twitter.com/niaidbioit> | @NIH3Dprint<https://twitter.com/nih3dprint>

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.

From: Hurt, Darrell (NIH/NIAID) [E]
Sent: Friday, September 22, 2017 6:48 AM
To: Healey, Joe <J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>>; David Bhella <David.Bhella at glasgow.ac.uk<mailto:David.Bhella at glasgow.ac.uk>>
Cc: NIH 3D Print Exchange <3Dprint at nih.gov<mailto:3Dprint at 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<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint>

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.

From: "Healey, Joe" <J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>>
Date: Friday, September 22, 2017 at 6:40 AM
To: David Bhella <David.Bhella at glasgow.ac.uk<mailto:David.Bhella at glasgow.ac.uk>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at 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 at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
________________________________
From: David Bhella <David.Bhella at glasgow.ac.uk<mailto:David.Bhella at glasgow.ac.uk>>
Sent: 22 September 2017 11:24:55
To: Healey, Joe
Cc: chimera-users at cgl.ucsf.edu<mailto:chimera-users at 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 at warwick.ac.uk<mailto:J.R.J.Healey at 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 at warwick.ac.uk<mailto:J.R.J.Healey at 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 at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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