[Chimera-users] Resolution of .stl file of ribbon representatiom

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Thu Apr 3 09:18:38 PDT 2014

Hi guys,

I think both of you have it. Gavin is right that simplifying the cross-section of the ribbon will reduce the triangle count. Tom is right that simply zooming out reduces the subdivisions along the ribbon (and therefore the triangle count). I'm using the "large_octagon" cross section preset and applying the "for3Dprint1round" scaling preset. Here's what I find:

Load up a PDB and hide any atoms that show up (so I'm considering only the ribbon)

File > Export without zooming: 4.2 MB X3D or 6.0 MB STL
File > Export with zoom-out: 2.0 MB X3D or 2.3 MB STL
File > Export without zooming but with scaling only: 4.7 MB X3D or 6.8 MB STL
File > Export with zoom-out and scaling only: 1.6 MB X3D or 1.6 MB STL
File > Export without zooming but with scaling and simple cross-section: 1.9 MB X3D or 2.7 MB STL
File > Export with zoom-out and scaling and simple cross-section: 898 KB X3D or 928 KB STL

When I view the meshes, it is apparent that zooming out does indeed reduce the subdivision frequency along the ribbon length and simplifying the ribbon cross section reduces the subdivision around the ribbon. It can be at least an 85% savings in triangle count!

Great tip!


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)

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From: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Date: Thursday, April 3, 2014 11:31 AM
To: Gavin Whittaker <g.whittaker at ed.ac.uk<mailto:g.whittaker at ed.ac.uk>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Resolution of .stl file of ribbon representatiom

Hi Gavin,

  The “subdivision” setting under “graphics quality” in the Effects dialog (menu Tools / Viewing Controls / Effects) controls the fineness of the ribbon mesh.  Actually it only controls the subdivisions along the ribbon.  I believe the standard round (oval) cross-section always has 20 subdivisions around the circumference no matter what the subdivision setting is.  So you may still need to use an external program to reduce the fineness.

  The default subdivision is I believe 1.5, and a lower value like 0.5 or 0.1 should reduce the ribbon stl file substantially.

  Aha, there is more to it.  The level of subdivision is intended to maintain good quality appearance on your display.  So when you zoom in the ribbon gets finer, and when you zoom out it gets coarser.  I just did a ltest, and when I export a ribbon where I am zoomed out so the protein only is an inch wide on my display the STL file is 3 Mbytes, but when I zoom in so the protein is 10 inches wide, the exported file is 18 Mbytes!  So siimply zooming out before you export will control fineness.  Again I believe that it only controls fineness along the length, with subdivisions around the circumference fixed.  When you export using different zoom levels the coordinates of the ribbon will not be shifted since zooming is just moving the camera closer or further away while the protein stays in the same place.


On Apr 3, 2014, at 2:48 AM, Gavin Whittaker  wrote:

Dear all,

   I'm in the process of 3d printing a large protein in ribbon format;  I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily.  I've managed to use other software to reduce the resolution of the mesh, so I can now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models?

  I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large.  One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective?


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