[Chimera-users] STL file questions

Tom Goddard goddard at sonic.net
Thu Sep 26 19:42:51 PDT 2013


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 at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Hurt, Darrell (NIH/NIAID) [E] 
> 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
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
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> 
> 
> 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?
>> 
>> 
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