From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed May 28 2014 - 11:53:36 CDT

Hello Darrell,

So I created an account and selected "create" . However, I have not been able to find a field that allows me to select ribbons as a model. In addition, it isn't clear from the pages how I can just create the printer file and use it to print my model.

Suggestions?

brian

-----Original Message-----
From: Hurt, Darrell (NIH/NIAID) [E] [mailto:darrellh_at_niaid.nih.gov]
Sent: Monday, May 19, 2014 7:50 AM
To: John Stone; Bennion, Brian
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: 3-d printing of vmd scenes

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:

http://3dprint.nih.gov

Cheers,
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 5/16/14 3:11 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
>Brian,
>  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?
>
>Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
>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 
>>breaking
>>    because the strands in the new cartoon rep are too thin.
>> 
>>    http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22001.html
>> 
>>    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
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>