3D printing a viral capsid
Hello I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed. I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure. You can see the model I’ve created here: https://dl.dropboxusercontent.com/u/9856122/CAPSID.py Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere. Any help would be lovely! Thanks! Jeremiah
Hi Jeremiah, I got a good import of your scene in Blender by exporting an OBJ from Chimera. Maybe give that a try. You can then convert to STL using Blender's tools. Hope it helps! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 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> 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: Jeremiah Gassensmith <jjg130230@utdallas.edu<mailto:jjg130230@utdallas.edu>> Date: Friday, August 22, 2014 10:15 AM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] 3D printing a viral capsid Hello I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed. I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure. You can see the model I’ve created here: https://dl.dropboxusercontent.com/u/9856122/CAPSID.py Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere. Any help would be lovely! Thanks! Jeremiah _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Jeremiah, The STL export of your virus capsid multiscale model is giving just one asymmetric unit and that is a Chimera bug. I’ll make a bug report and see if I can fix that. Here’s another suggestion about how to print it. Make a single density map for the entire capsid with the Chimera molmap command molmap #0 8 sym biomt This makes an 8 Angstrom resolution map using the asymmetric unit of the capsid PDB model #0 and uses the symmetry specified in the PDB file BIOMT remarks. I’ve attached an image of what it looks like. If you print on a single color printer this surface exported as STL is likely to work better than the Chimera Multiscale surfaces which may not be touching enough to hold together. Also it gives a better (and very different) appearance because it is single color. You can try different resolution values and see what works best. The resolution of 3d printers isn’t too good, so having too much detail doesn’t produce the best printed model. Tom On Aug 22, 2014, at 10:33 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi Jeremiah,
I got a good import of your scene in Blender by exporting an OBJ from Chimera. Maybe give that a try. You can then convert to STL using Blender's tools.
Hope it helps! Darrell
From: Jeremiah Gassensmith Date: Friday, August 22, 2014 10:15 AM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] 3D printing a viral capsid
Hello
I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed. I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure. You can see the model I’ve created here:
https://dl.dropboxusercontent.com/u/9856122/CAPSID.py
Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere. Any help would be lovely!
Thanks! Jeremiah
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Here’s the molmap capsid image. Tom On Aug 22, 2014, at 2:25 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Jeremiah,
The STL export of your virus capsid multiscale model is giving just one asymmetric unit and that is a Chimera bug. I’ll make a bug report and see if I can fix that.
Here’s another suggestion about how to print it. Make a single density map for the entire capsid with the Chimera molmap command
molmap #0 8 sym biomt
This makes an 8 Angstrom resolution map using the asymmetric unit of the capsid PDB model #0 and uses the symmetry specified in the PDB file BIOMT remarks. I’ve attached an image of what it looks like. If you print on a single color printer this surface exported as STL is likely to work better than the Chimera Multiscale surfaces which may not be touching enough to hold together. Also it gives a better (and very different) appearance because it is single color. You can try different resolution values and see what works best. The resolution of 3d printers isn’t too good, so having too much detail doesn’t produce the best printed model.
Tom
On Aug 22, 2014, at 10:33 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi Jeremiah,
I got a good import of your scene in Blender by exporting an OBJ from Chimera. Maybe give that a try. You can then convert to STL using Blender's tools.
Hope it helps! Darrell
From: Jeremiah Gassensmith Date: Friday, August 22, 2014 10:15 AM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] 3D printing a viral capsid
Hello
I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed. I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure. You can see the model I’ve created here:
https://dl.dropboxusercontent.com/u/9856122/CAPSID.py
Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere. Any help would be lovely!
Thanks! Jeremiah
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Jeremiah, I have fixed the Chimera export STL bug that caused your multiscale virus capsid model to produce STL that did not contain the whole virus. The fix will be in tonight’s daily build, dated August 23 (or later) on the Chimera download page. The bug was that copies of identical surfaces representing proteins were not having their individual position and rotation applied. Thanks for reporting the problem. Tom On Aug 22, 2014, at 7:15 AM, Jeremiah Gassensmith wrote:
Hello
I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed. I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure. You can see the model I’ve created here:
https://dl.dropboxusercontent.com/u/9856122/CAPSID.py
Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere. Any help would be lovely!
Thanks! Jeremiah
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Hurt, Darrell (NIH/NIAID) [E] -
Jeremiah Gassensmith -
Tom Goddard