VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 28 2014 - 14:31:10 CDT
As an aside, it would be neat if there was a way to submit jobs
to your web site from VMD to handle some of these special cases that
tools like VMD might not want to implement as a built-in feature.
If you have any interest in supporting a VMD plugin for this purpose
for arbitrary user-provided structure files, let us know.
On Wed, May 28, 2014 at 04:53:36PM +0000, Bennion, Brian wrote:
> 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.
> -----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:
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
> 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 5/16/14 3:11 PM, "John Stone" <johns_at_ks.uiuc.edu> 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
> > 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
> >> 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
> >http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/