From: Hurt, Darrell (NIH/NIAID) [E] (
Date: Mon May 19 2014 - 09:49:56 CDT

Hi everyone,

I don't want to derail this conversation too much, but I thought you might
want to know about the resource that we're developing for automatically
generating 3D print files from PDB files. It's currently in a public beta,
but we hope to formally launch in about a month. You can use it now.

As a registered user on the NIH 3D Print Exchange, it is simple to specify
a PDB accession code or upload a custom PDB and automatically generate
several different representations of that structure suitable for printing,
including "ribbon" models that include automatically-placed support
struts. This might be an easy solution to your problem. Check it out at:


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 <>
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On 5/16/14 3:11 PM, "John Stone" <> wrote:
>  What kind of solid material are you printing your models with?
>Is it one of the thermal plastic materials (spool-fed plastic "wire"
>put through a small heated nozzle), or is it something based on the
>build-up of 2-D printed layers?
>VMD itself doesn't know anything about building struts between
>parts of the model to strengthen it.  The way VMD currently works
>when exporting molecular scenes is that the same geometry shown on the
>screen is directly exported to an STL or VRML-2 or Wavefront OBJ file
>used as input to 3-D printing software.  It is clear that many of
>the existing VMD graphical representations are perhaps poorly suited
>to 3-D printing due to their inherent fragility.
>In the past, my recommendation has always been that the most robust
>way of creating 3-D models for printing is to use surface style
>representations, e.g. from QuickSurf, MSMS, or Surf.  These tend to
>work well with the 3-D printing software, and it is often pretty
>straightforward to choose atom selections that are both informative
>and result in a more robust solid model when printed.
>In principle it should be possible to teach VMD to be able to add
>"support struts" between parts of a molecular model, but it would
>require a fair amount of work, and I wonder if this might not be
>something that a 3-D printing program would do for itself, since
>this is generally an issue with all 3-D models, but the details of
>how much support are needed depend on the material being used for
>printing, and the scale of the model being printed.  What
>hardware/software are you using for your printing?
>  John Stone
>On Fri, May 16, 2014 at 05:49:05PM +0000, Bennion, Brian wrote:
>>    Hello
>>    I was curious if there were any vmd supported output types that
>>would add
>>    struts to 3D printed protein models.
>>    This link below was the latest mention of 3D printing but didn't
>>have any
>>    info on struts to make the models more robust.  Mine seem to be
>>    because the strands in the new cartoon rep are too thin.
>>    Brian
>NIH Center for Macromolecular Modeling and Bioinformatics
>Beckman Institute for Advanced Science and Technology
>University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>           Phone: 217-244-3349