Create an artificial bond between ribbons for 3D printing
Dear Chimera users, I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part. So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don’t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long. The only tool that would seem to come close to my requirement is the distance measure, however I can’t see how to convert that pseudo bond to a cylinder that will be exported. Any suggestions would be gratefully received. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research 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
Dear David, You can show pseudobonds as “stick” instead of lines. There are several routes; one way is to select the pseudobond(s) and then use the Selection Inspector: Ctrl-click on one, then up arrow to select all of them if there’s more than one, then click the green magnifying glass icon near the bottom right corner of the Chimera window. In the Selection Inspector, Inspect: Pseudobond, change bond style to stick. You can also edit the “radius” value. Another way is to use the “setattr” (set attribute) command: setattr p drawMode 1 setattr p radius .5 (you can find out the attribute names to use in this command by mousing over the corresponding settings in the Selection Inspector) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> There is also a “struts” command to automatically place strengthening pseudobonds and thicken the ribbons to make models more robust for 3D printing: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html> However, your approach of manually creating pseudobonds may also be effective. Besides using distance measurements, you can create a series of pseudobonds by listing the atom pairs in a text file and reading it in with Pseudobond Reader: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader....> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 28, 2015, at 6:47 AM, David Bhella <David.Bhella@glasgow.ac.uk> wrote:
Dear Chimera users, I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part. So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don’t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long.
The only tool that would seem to come close to my requirement is the distance measure, however I can’t see how to convert that pseudo bond to a cylinder that will be exported. Any suggestions would be gratefully received. Thanks, D.
Hi David, Chimera friends, please forgive me for stepping in here. Chimera is a terrific tool for preparing proteins for 3D printing. In fact, we use it at the NIH 3D Print Exchange to transform PDB and other files into 3D-printable objects. Although I'm sure that Elaine or others could give you some great advice about how to do this yourself in Chimera, I would also like to invite you to try the NIH 3D Print Exchange. Once you register (for free) you can use our "Create" tools to upload the PDB file of your trimer and get several different representations of your protein suitable for 3D printing, including a ribbon representation with the individual ribbons joined. If our automated tools are not sufficient for your purposes, I would be happy to share a few hints with you. For starters, I think the tool you want is called "struts" in Chimera: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/struts.html Hope that helps, Darrell -- Darrell Hurt, Ph.D. Acting Chief, Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A31 North Bethesda, MD 20892-2135 Office: 240-669-2741 Mobile: 301-758-3559Web: 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. On 4/28/15, 9:47 AM, "David Bhella" <David.Bhella@glasgow.ac.uk> wrote:
Dear Chimera users,
I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part. So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don¹t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long.
The only tool that would seem to come close to my requirement is the distance measure, however I can¹t see how to convert that pseudo bond to a cylinder that will be exported.
Any suggestions would be gratefully received.
Thanks, D.
Dr David Bhella MRC-University of Glasgow Centre for Virus Research 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Just to follow up, the NIH 3D Print Exchange URL is: http://3dprint.nih.gov On 4/28/15, 12:04 PM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov> wrote:
Hi David,
Chimera friends, please forgive me for stepping in here.
Chimera is a terrific tool for preparing proteins for 3D printing. In fact, we use it at the NIH 3D Print Exchange to transform PDB and other files into 3D-printable objects. Although I'm sure that Elaine or others could give you some great advice about how to do this yourself in Chimera, I would also like to invite you to try the NIH 3D Print Exchange. Once you register (for free) you can use our "Create" tools to upload the PDB file of your trimer and get several different representations of your protein suitable for 3D printing, including a ribbon representation with the individual ribbons joined.
If our automated tools are not sufficient for your purposes, I would be happy to share a few hints with you. For starters, I think the tool you want is called "struts" in Chimera: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/struts.html
Hope that helps, Darrell
-- Darrell Hurt, Ph.D. Acting Chief, Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
5601 Fishers Lane, 4A31 North Bethesda, MD 20892-2135 Office: 240-669-2741 Mobile: 301-758-3559Web: BCBB Home Page <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcb b .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.
On 4/28/15, 9:47 AM, "David Bhella" <David.Bhella@glasgow.ac.uk> wrote:
Dear Chimera users,
I am trying to prepare a ribbon diagram for 3D printing. As the molecule is a trimer, I would like to create a join between the ribbons such that the model is sent to the printer as a single part. So, I thought that I might be able to create a bond, but I suspect that the current tools may not be able to achieve this. Ideally I don¹t want to have to show side chains, moreover the bond needs to be preserved when exported as STL format and finally it will be quite long.
The only tool that would seem to come close to my requirement is the distance measure, however I can¹t see how to convert that pseudo bond to a cylinder that will be exported.
Any suggestions would be gratefully received.
Thanks, D.
Dr David Bhella MRC-University of Glasgow Centre for Virus Research 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
David Bhella -
Elaine Meng -
Hurt, Darrell (NIH/NIAID) [E]