[Chimera-users] STL file questions

Tom Goddard goddard at sonic.net
Thu Sep 26 17:09:37 PDT 2013


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
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