File formats/3D PDF

PDF documents with integrated 3D interactive models

Easy procedure

This is currently the easiest way to create a PDF document containing an interactive 3D molecular model, using only free software under Windows.

(This is a brief description; if needed, extra information may be found in the next section below)

1. Create a PDF document with the text and images from your preferred application (e.g. Word or Powerpoint), leaving enough blank spaces where you would position the 3D molecular models. If your application cannot export to PDF directly, you may use a virtual PDF printer like PDFforge PDF Creator or PDF-XChange Lite Printer (both available for free).
2. Download and install IDTFConverter; create a u3d.bat file for convenience (see below for addresses and details).
3. Download and install PDF-XChange Editor (free version); you need 8.0.332 at least (26 Aug. 2019)
4. Get a current version of Jmol. Open your molecule; display it in the desired orientation and style. Using the console, export the model to IDTF format: write myMol.idtf
5. Two files have been created: myMol.idtf and myMol.idtf.tex. Copy them to the folder where you have IDTFConverter, open the command line there and run the conversion: u3d.bat myMol. That will create a myMol.u3d
6. Open the previous PDF file into PDF-XChange Editor. Find the place where your left blank space. To insert a 3D annotation:
   • If you are using the Ribbon interface: Comment > Add 3D
   • If you are using the classical Toolbar interface: Tools > Media tools > Add or edit 3D annotations

   Draw the rectangle area with the mouse and pick your myMol.u3d file. Choose among the options offered for display, accept and save the file.

7. Check the 3D display in a PDF viewer application (note that only Adobe Reader and PDF-XChange Editor support this kind of 3D content)

Sample documents

This has been created following the above procedure

• Cysteine

Older reference

Installations

Jmol

You need at least version 12.0.RC26 to do this.

IDTF to U3D

(See also descriptions and comments for Jmol output to IDTF and U3D formats.)

Conversion from IDTF to U3D can be done using a simple command-line utility, IDTFConverter.

• Windows installation of IDTFConverter

1. The converter is available from Universal 3D Sample Software and from Michail Vidiassov's site (see refs. below). Download and unzip into, perhaps, c:\idtf\
2. Create a simple command file u3d.bat and place it in a folder where it is easily accessible (e.g. the Windows directory or a folder included in the system's path). This u3d.bat file must contain this text:

c:\idtf\idtfconverter.exe -input %1.idtf -output %1.u3d

• MacOS and Linux installation of IDTFConverter

1. You can get a port of IDTFConverter from Michail Vidiassov's site (see refs. below).
2. Create a command file similarly to the one described for Windows.

References

• Windows: Universal 3D Sample Software. Go to 'View All Files' and download the latest U3D_A_??.zip file.

You need to extract the contents of Bin/Win32/Release/: several files and the Plugins folder (that makes 4.46 MB out of the total 137 MB in the zipfile; you may probably dispense with the HelloWorld.exe, SamplePlayer.exe, TrueType.exe files).

• Windows: Alternatively, get just the necessary files from (broken link) http://www2.iaas.msu.ru/tmp/u3d/u3dIntelWin.zip (thanks to Michail Vidiassov).

You need to extract the contents of u3dIntelWin/: several files and the Plugins folder; the doc/ and samples/ folders are not essential (that makes 4.46 MB out of the total 29 MB in the zipfile; you may probably dispense with the HelloWorld.exe, SamplePlayer.exe, TrueType.exe files).

• MacOS and Linux: A port of the software is available as u3d-1.2.852.tar.gz or, possibly, a newer version, at (broken link) http://www2.iaas.msu.ru/tmp/u3d/ (thanks to Michail Vidiassov).

LaTeX to PDF

There are several pdfLatex software, like teTeX (Unix; discontinued in 2006), MiKTeX (Windows), TeX Live (Unix, Linux, Windows), MacTeX...

• Installation of MiKTeX (Windows)

1. Download and install MiKTeX "basic" from http://miktex.org/
2. Do an update (menu Programs > MiKTeX > Maintenance > Update).
3. Download the movie15 package (menu Programs > MikTex > Maintenance > Package Manager).

• You can avoid installing software and use instead an online service like ScribTeX (they have a Free Plan that gives you 50 MB storage space; you can even test-run it without signing up).

Creating the document

1. Within Jmol script console: write c:/temp/xxx.idtf

This will create two files: xxx.idtf and xxx.idtf.tex

Note: by default, the final PDF will be a letter-sized page (215.9×279.4 mm, 8.5×11 inches). If you want instead an A4-sized page (210×297 mm), edit now the xxx.idtf.tex file, look for the line that says

documentclass[12pt,letter]{article}

and replace with

documentclass[12pt,a4paper]{article}

2. At the system command line or terminal, call the u3d.bat file (Windows), or equivalent MacOS or Linux command file, to convert the .idtf to .u3d format:

u3d c:\temp\xxx

If using MikTeX:

3.1. Run the TeXworks program --included in MiKTeX-- and open in it your xxx.idtf.tex.

3.2. Click menu item Typeset > Typeset, or click on the green 'play'-like button (leftmost in the toolbar).

When processing ends, you will see a blank document in a new TeXworks window, because MiKTeX can't display the model, but xxx.idtf.pdf should have been created.

If using ScribTeX:

3.1. Go the ScribTeX website, sign up or use the guest account.

3.2. Click on [Upload file] and select in turn your xxx.idtf.tex and xxx.u3d files (or a .zip file containing both, it will be automatically unzipped in the server).

3.3. In the file listing on the server, click on the xxx.idtf.tex file to display it, then click on [Compile].

3.4. When the .pdf file opens in the browser, click on the [Save copy as] button in your viewer's toolbar, to store it in your local disk.

4. Open the .pdf file using a reader/viewer that supports 3D PDF (see a list below).

If you don't see the model in its panel inside the document, right-click on it and choose Partial options > Fit visible

Caveats

• If you move in Jmol the model rotation center away from screen center (as with CTRL-ALT-drag), the model in the 3D PDF will be a very close but not quite perfect reproduction. (The reason for this is that moving the center of perspective seems to be not supported in virtual reality formats like VRML and U3D.)
• Lighting is not working properly: the light moves with the model. If someone knows how to do that, please let us know.
• Perspective canot be orthographic from the beginning (Jmol uses this by default for crystal structures). Once in the 3D PDF, there is a right-mouse-button option to go into that mode. Please let us know if you know how to do that.
• Don't expect rotation and translation using the mouse in the 3D PDF to be like in Jmol. It is harder to control, and you can even completely loose the rotation center.
• For large models (big proteins, surfaces, electron density maps), files are quite big, and seeing and manipulating the model in the PDF will need substantial computer power. To alleviate this, you can try to set the image frequency to a lower value in the Reader's 3D options and/or to change the optimisation method for small frequency to 'Abandon'. Also, if you are using it in a presentation, it is a good idea to preload the PDF document in the Reader ahead of time.

Documents with text

In order to have text, images etc. alongside the 3D model, ideally you need a full PDF editor, which is normally commercial like Adobe Acrobat Pro.

As an alternative, some of the freeware PDF viewers, like PDF-XChange Editor, allow you to add text and images onto the generated 3D PDF and save the modified document.

The best freeware way to create a full pdf-presentation including 3D objects, text and other images is by using pdflatex with the Beamer package. See the Beamer wikipedia page for more information about Beamer.

Sample documents

(Text in these documents has been added externally to the process described here.)

• 3D PDF with an organic molecule, ball and stick.

File sizes were: .hin 5 kB; .idtf 121 kB; .u3d 47 kB; .pdf 18 kB.

• 3D PDF with a small protein, crambin (1crn.pdb), in cartoon rendering.
• 3D PDF with a polyhedra rendering of quartz.
• 3D PDF with a carbon nanotube, ball and stick and molecular surface.

File sizes were: .hin 16 kB; .idtf 1800 kB; .u3d 182 kB; .pdf 113 kB.

Software for creating or viewing 3D PDF

(This aims to be a compilation of resources; if you know of another software, please add it here).

3D PDF Viewers

• Adobe Reader v.7 or later (proprietary, freeware). Note that the latest Adobe Reader v.9 renders the 3D object more nicely than v.8 and v.7. In v.9 it is possible to remove the compass that appears by default in the lower left corner via the Reader's 3D content options.
• PDF-XChange Editor v.7.0.327 or later (from Tracker Software; proprietary, there is a free version). It can display 3D models embedded in the PDF if they were created in the U3D format (but currently not if created in the PRC format).
• There is a plug-in that allows Foxit Reader 9.1 or later to display 3D models.
• Most other PDF viewers are not able to display interactive 3D data.

3D PDF Editors

• Adobe Acrobat Pro Extended (proprietary, commercial).

Note that you do not create the 3D model using Adobe; you just insert or embed it from an available u3d file that you have prepared with another software (like Jmol + IDTFConverter). The Adobe editor will mainly serve to position the 3D model within the page and to insert the other content of the document.

• PDF-XChange Editor v.8.0.332 or later (from Tracker Software) can insert a 3D model from a U3D format file in an existing pdf document (also into a newly created blank document if you have the licensed version).
• Share3D PDF, by Quadrispace, looks like a promising solution to easily produce 3D-containing pdf documents at a reasonable price and with a nice set of features. Unfortunately, it doesn't seem to import any of the 3D formats that Jmol can produce.
• U3D-2-PDF seems to be a user-friendly freeware tool that drives MeshLab and MiKTeX to facilitate the procedure from a wrl file to a pdf document. (Requires MiKTeX, MeshLab and .NET Framework 4 installed; all freeware)

Bibliography

Related articles:

1. Grasping molecular structures through publication-integrated 3D models.

(2008) P. Kumar, A. Ziegler, J. Ziegler, B. Uchanska-Ziegler & A. Ziegler. Trends in Biochemical Sciences 33:408-412.

doi:j.tibs.2008.06.004

3DPDF version of the article (3.63 MB)

Here, we describe how an interactive 3D model of a molecular complex can be embedded directly into a PDF, thus providing readers with important and educational visual information that would otherwise be more difficult to disseminate.

They use Pymol + Adobe to produce the 3D PDF.

2. A step-by-step guide to creating PDF-integrated 3D models.

(Published online as Supplementary Material to #1)

Part 1: PyMOL ~ Part 2: Adobe 3D Reviewer ~ Part 3: PDF Export (Acrobat 9 Pro Extended)

http://www.charite.de/immungenetik/model3d.html

Pymol exports to VRML2; Adobe 3D Reviewer imports that and exports to U3D; Acrobat 9 Pro Extended is used to insert and finish off the 3D model in the PDF.

3. Incorporating interactive 3-dimensional graphics in astronomy research papers.

(2008) D. G. Barnes, C. J. Fluke. New Astronomy 13:599-605.

arXiv:0709.2734; doi:10.1016/j.newast.2008.03.008.

related wiki article.

The authors use the three dimensional plotting library S2PLOT to write a 3D object to VRML97 format and use then Adobe Acrobat 3D to embed it in a pdf document.

4. Leaving the structural ivory tower, assisted by interactive 3D PDF.

(2010) P. Kumar, A. Ziegler, A. Grahn, C.S. Hee, A. Ziegler. Trends Biochem. Sci. 35:419-422 doi:10.1016/j.tibs.2010.03.008.

5. Embedding and publishing interactive, 3-dimensional, scientific figures in portable document format (PDF) files.

(2013) D. Barnes, M. Vidiassov, B. Ruthensteiner, C. Fluke, M. Quayle, C. Colin. PLOS One 8:e69446 doi:10.1371/journal.pone.0069446.

They do not use the U3D format, but PRC instead.

6. Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files.

(2015) A. Newe. PeerJ 3:e794 doi:10.7717/peerj.794.

7. Enriching scientific publications with interactive 3D PDF: an integrated toolbox for creating ready-to-publish figures.

(2016) A. Newe. PeerJ Comput. Sci. 2:e64 doi:10.7717/peerj-cs.64.

8. On the use of PDF-3D to overcome spatial visualization difficulties linked with ternary phase diagrams.

(2019) D. Vergara, M. P. Rubio and M. Lorenzo. Education Sciences 9:67 doi:10.3390/educsci9020067.

Reports on generating 3D-PDF via OBJ file to (Adobe Photoshop) U3D to (Adobe Acrobat) PDF. Note: Jmol can export models to the OBJ format.

Contributors

AngelHerraez, Vdlee