Re: ChimeraX does not Support .stl files?
Hi Kevin, Please direct questions about ChimeraX to our mailing list, chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> — others on the team or even in the community may have more experience or more recent experience in a given subject than I or any other developer has at the moment. Eric (CC’ed) has been working on the NIH 3D pipeline; part of that pipeline is adding struts to delicate objects for 3D printing. He may be able to help you better than I can. — Zach
On 26 Jun 2024, at 14:55, Maroney, Kevin James <kmaroney@uab.edu> wrote:
Hello Dr. Pearson, Despite doing more Immunology research and really no proteomics, I have had a hobby interest in fooling around with Pymol and ChimeraX. I just recently got a very nice 3D Printer and was hoping to print out a model of the epitope of my PhD complexed between HLA-B57 and TCR that is publically available. I was going to use UCSF Chimera, but it does not seem like it is capable of representing space-filling diagrams and only gives me errors. I obviously can’t print the complex and delicate ribbon or atomic representations and like ChimeraX better anyway. But the guide from the NIH suggests passing PDB models through Chimera to generate .stl files which I can easily then pop into my Studio software to 3D print and resize etc. Problem is, I don’t see that there is any way to actually export as .stl in ChimeraX. Is there any way you could add this feature? Thank you very much. Lovely program.
Sincerely, Kevin Maroney M.S. Biotechnology University of California, Irvine PhD Student University of Alabama at Birmingham
Hi Kevin, Not sure where you are looking, but "stl" is indeed one of the save formats available from ChimeraX: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#top> Besides looking at the User Guide pages such as the above, you can get a list of all the save formats in the ChimeraX Log window with command "save formats" The links above were for the "save" command but you can also use the dialog opened with menu: File... Save. Of course there are many space-filling options (molecular surface, vdw spheres, etc.). You may want to try some tutorials to learn how to use ChimeraX. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> The "struts" command that Zach mentioned is if you are showing ribbons instead, it will add extra cylinders to strengthen the result for 3D printing and also has an option to make the ribbons fatter. Again see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html> See also 3D printed model gallery and links therein <https://www.rbvi.ucsf.edu/Outreach/technotes/ModelGallery/index.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2024, at 3:14 PM, Zach Pearson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Kevin,
Please direct questions about ChimeraX to our mailing list, chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> — others on the team or even in the community may have more experience or more recent experience in a given subject than I or any other developer has at the moment.
Eric (CC’ed) has been working on the NIH 3D pipeline; part of that pipeline is adding struts to delicate objects for 3D printing. He may be able to help you better than I can.
— Zach
On 26 Jun 2024, at 14:55, Maroney, Kevin James <kmaroney@uab.edu> wrote:
Hello Dr. Pearson, Despite doing more Immunology research and really no proteomics, I have had a hobby interest in fooling around with Pymol and ChimeraX. I just recently got a very nice 3D Printer and was hoping to print out a model of the epitope of my PhD complexed between HLA-B57 and TCR that is publically available. I was going to use UCSF Chimera, but it does not seem like it is capable of representing space-filling diagrams and only gives me errors. I obviously can’t print the complex and delicate ribbon or atomic representations and like ChimeraX better anyway. But the guide from the NIH suggests passing PDB models through Chimera to generate .stl files which I can easily then pop into my Studio software to 3D print and resize etc. Problem is, I don’t see that there is any way to actually export as .stl in ChimeraX. Is there any way you could add this feature? Thank you very much. Lovely program. <image001.png><image002.png> Sincerely, Kevin Maroney M.S. Biotechnology University of California, Irvine PhD Student University of Alabama at Birmingham
Hi Kevin, In addition to all of Elaine's excellent information, there is an "NIH Presets" bundle that you can install from the ChimeraX Toolshed (use Tools→More Tools... from the ChimeraX menus to install Toolshed bundles). The NIH Presets bundle has presets for preparing scenes for 3D printing by thickening ribbons, adding support struts, etc. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 26, 2024, at 4:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Kevin, Not sure where you are looking, but "stl" is indeed one of the save formats available from ChimeraX:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#top>
Besides looking at the User Guide pages such as the above, you can get a list of all the save formats in the ChimeraX Log window with command "save formats"
The links above were for the "save" command but you can also use the dialog opened with menu: File... Save.
Of course there are many space-filling options (molecular surface, vdw spheres, etc.). You may want to try some tutorials to learn how to use ChimeraX. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html>
The "struts" command that Zach mentioned is if you are showing ribbons instead, it will add extra cylinders to strengthen the result for 3D printing and also has an option to make the ribbons fatter. Again see the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html>
See also 3D printed model gallery and links therein <https://www.rbvi.ucsf.edu/Outreach/technotes/ModelGallery/index.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2024, at 3:14 PM, Zach Pearson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Kevin,
Please direct questions about ChimeraX to our mailing list, chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> — others on the team or even in the community may have more experience or more recent experience in a given subject than I or any other developer has at the moment.
Eric (CC’ed) has been working on the NIH 3D pipeline; part of that pipeline is adding struts to delicate objects for 3D printing. He may be able to help you better than I can.
— Zach
On 26 Jun 2024, at 14:55, Maroney, Kevin James <kmaroney@uab.edu> wrote:
Hello Dr. Pearson, Despite doing more Immunology research and really no proteomics, I have had a hobby interest in fooling around with Pymol and ChimeraX. I just recently got a very nice 3D Printer and was hoping to print out a model of the epitope of my PhD complexed between HLA-B57 and TCR that is publically available. I was going to use UCSF Chimera, but it does not seem like it is capable of representing space-filling diagrams and only gives me errors. I obviously can’t print the complex and delicate ribbon or atomic representations and like ChimeraX better anyway. But the guide from the NIH suggests passing PDB models through Chimera to generate .stl files which I can easily then pop into my Studio software to 3D print and resize etc. Problem is, I don’t see that there is any way to actually export as .stl in ChimeraX. Is there any way you could add this feature? Thank you very much. Lovely program. <image001.png><image002.png> Sincerely, Kevin Maroney M.S. Biotechnology University of California, Irvine PhD Student University of Alabama at Birmingham
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Zach Pearson