Hi, I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information. Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property). Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ? -- David Gene Morgan Electron Microscopy Center 320C Simon Hall IU Bloomington 812 856 1457 (office) 812 856 3221 (3200) http://bio.indiana.edu/~cryo
Hi David, The STL (STereoLithography) file format does not include colors. There are hacks to the format that add colors but Chimera does not implement that. The STL file format wikipedia article describes them. http://en.wikipedia.org/wiki/STL_(file_format) Chimera File / Export to stl puts out exactly the number of triangles it is currently to render on screen. For density maps you can use the "step" paramter in the volume viewer dialog to reduce the number of triangles. Step 2 will take every other data point along each of the 3 axes and compute a contour surface. That will reduce the number of triangles approximately 4-fold versus the full resolution step 1 setting. Likewise step 4 would reduce triangle count by a factor of about 16 (= step*step). For molecule model the ribbons, and atom spheres, and cylinder bonds have the number of triangles controlled by "subdivision quality" which is set using menu Tools / Viewing Controls / Effects. Again I believe that scales the 1-dimensional subdivision, so 3 times higher subdivision means 9 times more triangles. The scaling is only approximate since there are some minimum number of triangles per sphere or cylinder. Also I think ribbons only scale the subdivisions along the length, always having 20 subdivision around the circumference of a cross-section. So ribbon triangle count may scale only linearly with subdivision value. The units for the STL file are Angstroms if that is what you are using in Chimera. PDB molecule structures are always Angstroms. Density maps can have their grid spacing specified in the volume viewer dialog (Features / Coordinates / voxel size) and you could use units of nanometers or anything you like, although if you use anything other than Angstroms then density maps won't have the correct scale compared to superposed PDB models. Here are some 3-d printed models we made. http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html If you have a printer that makes fragile models (most color printers) then you might me interested in my recent addition of the "struts" command that adds bonds to brace molecular models. http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009063.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html Tom On Sep 26, 2013, at 10:19 AM, David Gene Morgan wrote:
Hi,
I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information.
Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property).
Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ?
-- David Gene Morgan Electron Microscopy Center 320C Simon Hall IU Bloomington 812 856 1457 (office) 812 856 3221 (3200) http://bio.indiana.edu/~cryo _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi David, I can answer the first couple of questions: The STL export does not include color, dots, lines, or text, in addition to sharing the limitations listed for VRML and X3D. Limitations of all three are given in: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html> As for number of triangles, there is some control, but details depend on what you are exporting. See the "Smoothness" section in the image tips: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> I'm hoping someone else can weigh in on the scaling issue. 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 Sep 26, 2013, at 10:19 AM, David Gene Morgan <dagmorga@indiana.edu> wrote:
Hi, I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information.
Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property).
Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ?
Hi everyone, STLs and most other mesh objects are analogous to 2D "vector graphics" that are defined by vertices, edges, and faces. The STL format is an example of this. It uses units, but they are "STL units". It is up to you to assign those units a real-world measure (inches, millimeters, etc.) when you import them for 3D printing. When Chimera exports an STL, the units used in the resulting STL files are those of Chimera (Angstroms). I used Blender to import an STL created by Chimera. I verified that the units were imported one-to-one into "Blender units" (this is also how I verified that the output units of Chimera are Angstroms). I imported several STL files created by Chimera into Blender and their relative sizes and orientations were maintained. Therefore, when you import an STL generated by Chimera into your 3D printing software, if you assign the units to be inches, the resulting scale of the object is: 10^-10 * scale = 2.54*10^-2 scale = 2.54*10^-2/10^-10 = 2.54*10^8 or ~254 million At this scale, the resulting print for even a small protein can be 20+ inches! For this reason, I usually size the molecule down to 10% of the imported size to get a reasonable-sized print. Therefore the scale becomes ~25 million. If you assign the units to be millimeters, then the scale is: 10^-10 * scale = 10^-3 scale = 10^-3/10^-10 = 10^7 or 10 million Hope that 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: 301-758-3559Web: 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> 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 9/26/13 8:16 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi David, I can answer the first couple of questions:
The STL export does not include color, dots, lines, or text, in addition to sharing the limitations listed for VRML and X3D. Limitations of all three are given in:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
As for number of triangles, there is some control, but details depend on what you are exporting. See the "Smoothness" section in the image tips:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
I'm hoping someone else can weigh in on the scaling issue.
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 Sep 26, 2013, at 10:19 AM, David Gene Morgan <dagmorga@indiana.edu> wrote:
Hi, I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information.
Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property).
Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ?
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I would also recommend running the stl through meshlab before printing. Meshlab will allow you to correct for anomalies and errors. It will also do simplification of vertices, fix holes, search for problems, etc.; things that can cause the printer to generate garbage if not caught. There are a lot of things you can get away with in graphics that don't fly with 3D printers. http://meshlab.sourceforge.net/ Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Hurt, Darrell (NIH/NIAID) [E] [darrellh@niaid.nih.gov] Sent: Thursday, September 26, 2013 8:47 PM To: chimera-users@cgl.ucsf.edu List; David Gene Morgan Subject: Re: [Chimera-users] STL file questions Hi everyone, STLs and most other mesh objects are analogous to 2D "vector graphics" that are defined by vertices, edges, and faces. The STL format is an example of this. It uses units, but they are "STL units". It is up to you to assign those units a real-world measure (inches, millimeters, etc.) when you import them for 3D printing. When Chimera exports an STL, the units used in the resulting STL files are those of Chimera (Angstroms). I used Blender to import an STL created by Chimera. I verified that the units were imported one-to-one into "Blender units" (this is also how I verified that the output units of Chimera are Angstroms). I imported several STL files created by Chimera into Blender and their relative sizes and orientations were maintained. Therefore, when you import an STL generated by Chimera into your 3D printing software, if you assign the units to be inches, the resulting scale of the object is: 10^-10 * scale = 2.54*10^-2 scale = 2.54*10^-2/10^-10 = 2.54*10^8 or ~254 million At this scale, the resulting print for even a small protein can be 20+ inches! For this reason, I usually size the molecule down to 10% of the imported size to get a reasonable-sized print. Therefore the scale becomes ~25 million. If you assign the units to be millimeters, then the scale is: 10^-10 * scale = 10^-3 scale = 10^-3/10^-10 = 10^7 or 10 million Hope that 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: 301-758-3559Web: 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> 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 9/26/13 8:16 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi David, I can answer the first couple of questions:
The STL export does not include color, dots, lines, or text, in addition to sharing the limitations listed for VRML and X3D. Limitations of all three are given in:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
As for number of triangles, there is some control, but details depend on what you are exporting. See the "Smoothness" section in the image tips:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
I'm hoping someone else can weigh in on the scaling issue.
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 Sep 26, 2013, at 10:19 AM, David Gene Morgan <dagmorga@indiana.edu> wrote:
Hi, I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information.
Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property).
Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ?
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Matt, Your comment reminds me that I fixed a Chimera export bug where the end caps of molecule ribbons had triangle vertices in the wrong order, causing our uPrint software (Catalyst 4.4) to reject the file. I fixed this bug in the Chimera daily builds. So use a daily build if you are trying to print ribbons. Tom On Sep 26, 2013, at 7:06 PM, "Dougherty, Matthew T" wrote:
I would also recommend running the stl through meshlab before printing. Meshlab will allow you to correct for anomalies and errors. It will also do simplification of vertices, fix holes, search for problems, etc.; things that can cause the printer to generate garbage if not caught. There are a lot of things you can get away with in graphics that don't fly with 3D printers.
http://meshlab.sourceforge.net/
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Hurt, Darrell (NIH/NIAID) [E] Sent: Thursday, September 26, 2013 8:47 PM To: chimera-users@cgl.ucsf.edu List; David Gene Morgan Subject: Re: [Chimera-users] STL file questions
Hi everyone,
STLs and most other mesh objects are analogous to 2D "vector graphics" that are defined by vertices, edges, and faces. The STL format is an example of this. It uses units, but they are "STL units". It is up to you to assign those units a real-world measure (inches, millimeters, etc.) when you import them for 3D printing.
When Chimera exports an STL, the units used in the resulting STL files are those of Chimera (Angstroms). I used Blender to import an STL created by Chimera. I verified that the units were imported one-to-one into "Blender units" (this is also how I verified that the output units of Chimera are Angstroms). I imported several STL files created by Chimera into Blender and their relative sizes and orientations were maintained.
Therefore, when you import an STL generated by Chimera into your 3D printing software, if you assign the units to be inches, the resulting scale of the object is: 10^-10 * scale = 2.54*10^-2 scale = 2.54*10^-2/10^-10 = 2.54*10^8 or ~254 million
At this scale, the resulting print for even a small protein can be 20+ inches! For this reason, I usually size the molecule down to 10% of the imported size to get a reasonable-sized print. Therefore the scale becomes ~25 million.
If you assign the units to be millimeters, then the scale is: 10^-10 * scale = 10^-3 scale = 10^-3/10^-10 = 10^7 or 10 million
Hope that 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: 301-758-3559Web: 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>
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 9/26/13 8:16 PM, "Elaine Meng" wrote:
Hi David, I can answer the first couple of questions:
The STL export does not include color, dots, lines, or text, in addition to sharing the limitations listed for VRML and X3D. Limitations of all three are given in:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
As for number of triangles, there is some control, but details depend on what you are exporting. See the "Smoothness" section in the image tips:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
I'm hoping someone else can weigh in on the scaling issue.
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 Sep 26, 2013, at 10:19 AM, David Gene Morgan wrote:
Hi, I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information.
Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property).
Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ?
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (5)
-
David Gene Morgan -
Dougherty, Matthew T -
Elaine Meng -
Hurt, Darrell (NIH/NIAID) [E] -
Tom Goddard