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-rese... https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.p... 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! [cid:image003.jpg@01D33385.D40FF980] 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@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<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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> Date: Friday, September 22, 2017 at 6:40 AM To: David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto: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<mailto:J.R.J.Healey@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@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Sent: 22 September 2017 11:24:55 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu<mailto: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<mailto: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<mailto: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<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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-rese... https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.p... 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! [cid:image003.jpg@01D33385.D40FF980] 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@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<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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> Date: Friday, September 22, 2017 at 6:40 AM To: David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto: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<mailto:J.R.J.Healey@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@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Sent: 22 September 2017 11:24:55 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu<mailto: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<mailto: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<mailto: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<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@warwick.ac.uk] Sent: Friday, September 22, 2017 10:11 AM To: Tyrwhitt-Drake, James (NIH/NIAID) [C] <james.tyrwhitt-drake@nih.gov>; Hurt, Darrell (NIH/NIAID) [E] <darrellh@niaid.nih.gov>; David Bhella <David.Bhella@glasgow.ac.uk> Cc: NIH 3D Print Exchange <3Dprint@nih.gov>; chimera-users@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@warwick.ac.uk<mailto:J.R.J.Healey@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@nih.gov<mailto:james.tyrwhitt-drake@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@cgl.ucsf.edu<mailto:chimera-users@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-rese... https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.p... 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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>>; David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: NIH 3D Print Exchange <3Dprint@nih.gov<mailto: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<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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> Date: Friday, September 22, 2017 at 6:40 AM To: David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto: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<mailto:J.R.J.Healey@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@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Sent: 22 September 2017 11:24:55 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu<mailto: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<mailto: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<mailto: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<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi James et al., Reading the document, for repair of STL files, there is the recommendation to use Netfabb, it appears to only be available for Windows however, do you have a recommendation for MacOS alternatives? Thanks for all your help everyone! 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<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@nih.gov> Sent: 22 September 2017 15:36:32 To: Healey, Joe; Hurt, Darrell (NIH/NIAID) [E]; David Bhella Cc: NIH 3D Print Exchange; chimera-users@cgl.ucsf.edu Subject: RE: [Chimera-users] STL File export size 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@warwick.ac.uk] Sent: Friday, September 22, 2017 10:11 AM To: Tyrwhitt-Drake, James (NIH/NIAID) [C] <james.tyrwhitt-drake@nih.gov>; Hurt, Darrell (NIH/NIAID) [E] <darrellh@niaid.nih.gov>; David Bhella <David.Bhella@glasgow.ac.uk> Cc: NIH 3D Print Exchange <3Dprint@nih.gov>; chimera-users@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@warwick.ac.uk<mailto:J.R.J.Healey@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@nih.gov<mailto:james.tyrwhitt-drake@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@cgl.ucsf.edu<mailto:chimera-users@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-rese... https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.p... 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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>>; David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: NIH 3D Print Exchange <3Dprint@nih.gov<mailto: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<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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> Date: Friday, September 22, 2017 at 6:40 AM To: David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto: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<mailto:J.R.J.Healey@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@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Sent: 22 September 2017 11:24:55 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu<mailto: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<mailto: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<mailto: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<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Joe, We currently repair STL atomic structure models using Microsoft's online Tools3D site as described in Tom Ferrin’s message below. Since it is online that step could be done from a Mac (use Firefox, Safari does not allow upload for some reason). You need a Microsoft account and it asks you to give permission to share all your email contacts, or some such non-sense and does not let you proceed unless you say yes. I don’t understand that because it does not have access to those contacts since I don’t install anything on my machine, so I judged it harmless although annoying. The Microsoft repair supposedly uses Autodesk and netfabb in the cloud. We used an academic free version of Autodesk (on Windows only) to get similar results with more effort. The Microsoft tool does not return STL, instead giving a .3mf file which needs to be converted to STL. That can be done (on Window) with the Microsoft 3D Builder app. At any rate, this whole process works ok on Windows and produces a good quality mesh removing intersections of ribbons, atom spheres, and bond cylinders to produce a single closed mesh that the 3D printer software can handle. Tom
Begin forwarded message:
From: Tom Ferrin Subject: Protocol for 3D printing from ChimeraX Date: September 13, 2017 at 5:30:18 PM PDT To: Tom Goddard
1) Create the desired molecular display in ChimeraX and save as an STL file.
2) Upload the file to Microsoft's free "Tools3D" web site, tools3d.azurewebsites.net and click the repair button. Then save the repaired file on you desktop (it will have a .3mf file extension).
3) Download and install the "3D Builder" application, available for free at the Microsoft online store, and then open the repaired .3mf file and export it as a .stl file.
4) Open the .stl file in Catalyst and print. In Catalyst we always click on the Orientation tab and then the Optimize button before building the toolpath layers, as this minimizes the amount of support material used by the printer.
—t
om
On Sep 23, 2017, at 3:38 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:
Hi James et al.,
Reading the document, for repair of STL files, there is the recommendation to use Netfabb, it appears to only be available for Windows however, do you have a recommendation for MacOS alternatives?
Thanks for all your help everyone!
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 <mailto:J.R.J.Healey@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 <http://orcid.org/0000-0002-9569-6738>
Hi Joe, I'm with the team at NIH. Just a quick note that Chimera exports X3D files, and we provide those for download as well. X3D are typically 1/5th the size of an STL, and you can use them with Cura, or any software based on the Cura slicing engine. Best, Meghan ------------------------------- Meghan Coakley McCarthy, Ph.D. Project Lead, NIH 3D Print Exchange Bioinformatics and Computational Biosciences Branch (BCBB) NIH/NIAID/OD/OSMO/OCICB Contractor, Medical Science and Computing, Inc. 5601 Fishers Lane<x-apple-data-detectors://1>, Room 4A33A Rockville, MD 20892-9815<x-apple-data-detectors://2/0> O: 240.669.2753<tel:240.669.2753> | M: 240.507.6485<tel:240.507.6485> @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. This is a pre-decisional document. On Sep 22, 2017, at 10:12 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> wrote: 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@warwick.ac.uk<mailto:J.R.J.Healey@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<http://orcid.org/0000-0002-9569-6738> ________________________________ From: Tyrwhitt-Drake, James (NIH/NIAID) [C] <james.tyrwhitt-drake@nih.gov<mailto:james.tyrwhitt-drake@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@cgl.ucsf.edu<mailto:chimera-users@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-rese... https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.p... 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! [cid:image003.jpg@01D33385.D40FF980] 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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>>; David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: NIH 3D Print Exchange <3Dprint@nih.gov<mailto: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<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@warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> Date: Friday, September 22, 2017 at 6:40 AM To: David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto: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<mailto:J.R.J.Healey@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<http://orcid.org/0000-0002-9569-6738> ________________________________ From: David Bhella <David.Bhella@glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Sent: 22 September 2017 11:24:55 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu<mailto: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<mailto: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<mailto: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<http://orcid.org/0000-0002-9569-6738> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Healey, Joe -
McCarthy, Meghan (NIH/NIAID) [C] -
Tom Goddard -
Tyrwhitt-Drake, James (NIH/NIAID) [C]