From: Hurt, Darrell (NIH/NIAID) [E] (darrellh_at_niaid.nih.gov)
Date: Wed May 28 2014 - 15:04:24 CDT

Hi Brian,

Our "Create" tools are meant for relatively nave users. When you upload a PDB or specify a PDB identifier, our tools auto-generate two representations of the protein: one is a ribbon structure with all the ligands and their coordinating side chains displayed as sticks and the other is a surface structure of the amino and/or nucleic acids only. The ribbon structure also contains supporting "struts" that are mechanical only they do not represent hydrogen bonds or any other physical, chemical, or biological relationships. We generate these two structures using a variety of coloring schemes. The ribbons have four coloring schemes: monochrome, "rainbow" (blue-to-red for N- to C-termini), colored by secondary structure (helices, sheets, etc.), and colored by chain. The surfaces have three coloring schemes: monochrome, "coulombic" (a quick-and-dirty electrostatic potential approximation), and "hydropathy" (residues colored by Kyte-Doolittle hydropathy values). In this way, we create seven different variants for
download using a single PDB upload or submission. All you have to do is upload the PDB or specify an identifier and we do all the rest.

We may someday implement the ability to highlight specific residues for representation as sticks or coloring in the future, but at the present time we have no ability to accommodate that. However, you can generate a custom VRML file and upload that to share. We are still exploring new ways to represent uploaded structures. If you have suggestions, we would love to hear them.

Hope this helps,
Darrell

--
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
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From: <Bennion>, Brian <Bennion1_at_llnl.gov<mailto:Bennion1_at_llnl.gov>>
Date: Wednesday, May 28, 2014 12:53 PM
To: Darrell Hurt <darrellh_at_niaid.nih.gov<mailto:darrellh_at_niaid.nih.gov>>
Cc: "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>" <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: RE: vmd-l: 3-d printing of vmd scenes
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<mailto: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
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559Web: BCBB Home Page
<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb
.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit <https://twitter.com/niaidbioit>
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
On 5/16/14 3:11 PM, "John Stone" <johns_at_ks.uiuc.edu<mailto: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<mailto: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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/