Hello ChimeraX, I wanted to reach out and inquire about the ChimeraX tool. I see that it has the ability to save in multiple different formats, but I have a question about conversion into alternative formats. I found details about this tool looking for a PDB to STL file conversion and came across this page: https://www.cgl.ucsf.edu/chimerax/ and looking at the filetypes you interact with listed on this page: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html I see that it works with PDB files, which are used for modeling in some VR and AR environments such as Calcflow and Nanome. Would ChimeraX have the ability to import PDB files and export them as STL files for 3D printing? I ask this as I research ways to make AR and VR more accessible to classrooms. Sincerely, Joshua Hori Accessible Technology Coordinator Information Educational Technology Academic Technology Services 50 Hutchison Dr. Davis, CA 95616 530-752-2439 Schedule a meeting via Calendly<https://calendly.com/d/ytt-hsj-vbn>
Hi Joshua, Yes ChimeraX can read PDB and output STL for 3D printing (single color, since STL does not include colors) or for other uses. For example use ChimeraX commands to open a PDB model and save as STL open 8ja4 save pdb_8ja4.stl ChimeraX also outputs GLTF (.glb files) which includes color information and may be useful for 3D printing. There are lots choices for styles (spheres, ribbons, surfaces) and coloring of PDB atomic models. For styles like ribbons that would be too fragile to print you may add struts with the ChimeraX struts command. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/struts.html ChimeraX also directly can use virtual reality headsets, either standalone with Quest 2,3,Pro https://www.rbvi.ucsf.edu/chimerax/data/looksee-mar2023/looksee.html or connected to a Windows PC https://www.cgl.ucsf.edu/chimerax/docs/user/vr.html I recommend the standalone use since it can be used with any computer (e.g. Mac laptop) to send molecular models to Quest headsets. Tom
On May 13, 2024, at 12:52 PM, Joshua Hori via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX,
I wanted to reach out and inquire about the ChimeraX tool. I see that it has the ability to save in multiple different formats, but I have a question about conversion into alternative formats.
I found details about this tool looking for a PDB to STL file conversion and came across this page: https://www.cgl.ucsf.edu/chimerax/ and looking at the filetypes you interact with listed on this page: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
I see that it works with PDB files, which are used for modeling in some VR and AR environments such as Calcflow and Nanome. Would ChimeraX have the ability to import PDB files and export them as STL files for 3D printing? I ask this as I research ways to make AR and VR more accessible to classrooms.
Sincerely,
Joshua Hori Accessible Technology Coordinator Information Educational Technology Academic Technology Services 50 Hutchison Dr. Davis, CA 95616 530-752-2439 Schedule a meeting via Calendly <https://calendly.com/d/ytt-hsj-vbn>
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thanks for the prompt response Tom! I’ll be sharing these details in slack as well for those interested in making digital platforms accessible. I’m sharing this with our TEAM’s Lab, which is our 3D printing prototype lab. We have a construction cost analysis course that is conducted in AR which I would like to export and 3D print for accommodation purposes. This would make it so that blind, low vision, and aphantasia students can interact with course content in other ways. Sincerely, Joshua Hori Accessible Technology Coordinator Information Educational Technology Academic Technology Services 50 Hutchison Dr. Davis, CA 95616 530-752-2439 Schedule a meeting via Calendly<https://calendly.com/d/ytt-hsj-vbn> From: Tom Goddard <goddard@sonic.net> Date: Monday, May 13, 2024 at 1:47 PM To: Joshua Hori <jhori@ucdavis.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Questions about ChimeraX Hi Joshua, Yes ChimeraX can read PDB and output STL for 3D printing (single color, since STL does not include colors) or for other uses. For example use ChimeraX commands to open a PDB model and save as STL open 8ja4 save pdb_8ja4.stl ChimeraX also outputs GLTF (.glb files) which includes color information and may be useful for 3D printing. There are lots choices for styles (spheres, ribbons, surfaces) and coloring of PDB atomic models. For styles like ribbons that would be too fragile to print you may add struts with the ChimeraX struts command. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/struts.html ChimeraX also directly can use virtual reality headsets, either standalone with Quest 2,3,Pro https://www.rbvi.ucsf.edu/chimerax/data/looksee-mar2023/looksee.html or connected to a Windows PC https://www.cgl.ucsf.edu/chimerax/docs/user/vr.html I recommend the standalone use since it can be used with any computer (e.g. Mac laptop) to send molecular models to Quest headsets. Tom On May 13, 2024, at 12:52 PM, Joshua Hori via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello ChimeraX, I wanted to reach out and inquire about the ChimeraX tool. I see that it has the ability to save in multiple different formats, but I have a question about conversion into alternative formats. I found details about this tool looking for a PDB to STL file conversion and came across this page: https://www.cgl.ucsf.edu/chimerax/ and looking at the filetypes you interact with listed on this page: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html I see that it works with PDB files, which are used for modeling in some VR and AR environments such as Calcflow and Nanome. Would ChimeraX have the ability to import PDB files and export them as STL files for 3D printing? I ask this as I research ways to make AR and VR more accessible to classrooms. Sincerely, Joshua Hori Accessible Technology Coordinator Information Educational Technology Academic Technology Services 50 Hutchison Dr. Davis, CA 95616 530-752-2439 Schedule a meeting via Calendly<https://calendly.com/d/ytt-hsj-vbn> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Joshua, ChimeraX is used by the NIH to make a database of printable 3D models of molecules, cells, tissues, organs... called NIH 3D. The models are free to download here https://3d.nih.gov/ Several years ago the ChimeraX team at UCSF was printing 3D molecular models. Here are some examples https://www.rbvi.ucsf.edu/Outreach/technotes/ModelGallery/index.html Tom
On May 13, 2024, at 2:08 PM, Joshua Hori via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks for the prompt response Tom! I’ll be sharing these details in slack as well for those interested in making digital platforms accessible.
I’m sharing this with our TEAM’s Lab, which is our 3D printing prototype lab. We have a construction cost analysis course that is conducted in AR which I would like to export and 3D print for accommodation purposes. This would make it so that blind, low vision, and aphantasia students can interact with course content in other ways.
Sincerely,
Joshua Hori Accessible Technology Coordinator Information Educational Technology Academic Technology Services 50 Hutchison Dr. Davis, CA 95616 530-752-2439 Schedule a meeting via Calendly <https://calendly.com/d/ytt-hsj-vbn>
From: Tom Goddard <goddard@sonic.net> Date: Monday, May 13, 2024 at 1:47 PM To: Joshua Hori <jhori@ucdavis.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Questions about ChimeraX
Hi Joshua,
Yes ChimeraX can read PDB and output STL for 3D printing (single color, since STL does not include colors) or for other uses. For example use ChimeraX commands to open a PDB model and save as STL
open 8ja4 save pdb_8ja4.stl
ChimeraX also outputs GLTF (.glb files) which includes color information and may be useful for 3D printing. There are lots choices for styles (spheres, ribbons, surfaces) and coloring of PDB atomic models. For styles like ribbons that would be too fragile to print you may add struts with the ChimeraX struts command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/struts.html
ChimeraX also directly can use virtual reality headsets, either standalone with Quest 2,3,Pro
https://www.rbvi.ucsf.edu/chimerax/data/looksee-mar2023/looksee.html
or connected to a Windows PC
https://www.cgl.ucsf.edu/chimerax/docs/user/vr.html
I recommend the standalone use since it can be used with any computer (e.g. Mac laptop) to send molecular models to Quest headsets.
Tom
On May 13, 2024, at 12:52 PM, Joshua Hori via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX,
I wanted to reach out and inquire about the ChimeraX tool. I see that it has the ability to save in multiple different formats, but I have a question about conversion into alternative formats.
I found details about this tool looking for a PDB to STL file conversion and came across this page: https://www.cgl.ucsf.edu/chimerax/ and looking at the filetypes you interact with listed on this page: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
I see that it works with PDB files, which are used for modeling in some VR and AR environments such as Calcflow and Nanome. Would ChimeraX have the ability to import PDB files and export them as STL files for 3D printing? I ask this as I research ways to make AR and VR more accessible to classrooms.
Sincerely,
Joshua Hori Accessible Technology Coordinator Information Educational Technology Academic Technology Services 50 Hutchison Dr. Davis, CA 95616 530-752-2439 Schedule a meeting via Calendly <https://calendly.com/d/ytt-hsj-vbn>
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Joshua Hori -
Tom Goddard