[Chimera-users] STL file questions

Dougherty, Matthew T matthewd at bcm.edu
Thu Sep 26 19:06:00 PDT 2013

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.


Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
From: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Hurt, Darrell (NIH/NIAID) [E] [darrellh at niaid.nih.gov]
Sent: Thursday, September 26, 2013 8:47 PM
To: chimera-users at 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 Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559Web: BCBB Home Page
Twitter: @niaidbioit <https://twitter.com/niaidbioit>

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On 9/26/13 8:16 PM, "Elaine Meng" <meng at 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:
>I'm hoping someone else can weigh in on the scaling issue.
>I hope this helps,
>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 at indiana.edu>
>> 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
>>      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 at cgl.ucsf.edu

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