Latest revision as of 12:30, 26 March 2026

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 (at least free in Windows; solutions for the Mac need more investigation to confirm).

Downloads

Windows and MacOS: download the graphic user interface version of IDTFConverter from the Jmol website:
- Windows: download the IDTF_U3D_Converter.zip, unpack the zip file and put the single IDTF_U3D_Converter.exe file wherever you want in your local disk. If you find it convenient, create a shortcut for it in the desktop or the Start menu.
- MacOS: choose and download the app suitable for your system:
  - IDTF_U3D_Converter_Intel.zip if your computer is based on an Intel processor. Unpack the zip file to obtain the executable file, IDTF_U3D_Converter.app
  - IDTF_U3D_Converter_Silicon.zip if your computer is based on a Silicon processor (usually ARM). Unpack the zip file to obtain the executable file, IDTF_U3D_Converter.app

Create the IDTF file

Get a current version of Jmol application. Open your molecule; display it in the desired orientation and style.
- Suggestion: make the Jmol window square, using top menu > Display > Resize and entering two equal numbers. The result will look better if you insert it later into a square box within the pdf.
- Note: you can also do it with JSmol embedded in some webpage. Generation of the idtf file may take longer, though, if the model is complex.
If the export to IDTF option has been implemented in the menu:
- Top menu bar > File > Export > Export to IDTF
- Pop-up context menu > File > Export > Export IDTF 3D model
Otherwise, open the console and enter write myMol.idtf
Two files will be created: myMol.idtf and myMol.idtf.tex. For the current method, you may discard the .tex file.

Create the U3D file

Open the IDTF_U3D_Converter program or app, browse to load your .idtf file, choose the output folder and click on "Convert". The output will have the same filename as the input, with extension .u3d

Prepare your PDF document

Use your preferred program (word processor, presentation, ...) to create a document with text and images, leaving square space(s) where you will later insert the 3D molecular models, and export to pdf format.
- 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).
To insert the 3D models you need a pdf editor that is compatible with the 3D-PDF standard. Examples: Adobe Acrobat Pro and PDF-XChange Editor (Windows-only, free or paid version)
In PDF-XChange Editor: open the previous PDF, find the place where your left blank space. To insert a 3D annotation there:
- 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. Suggestion: draw a square by holding the Shift key while dragging to define the area.
- In 3D Artwork, select your myMol.u3d file.
- Choose among any other display options offered (like activation of the content, border and background color)
- Accept and save the file.
In Adobe Acrobat Pro: open the previous PDF, find the place where your left a blank space. To insert 3D media there:
- From the upper left of the screen, select All tools > Add rich media > 3D media.
- Drag a rectangle (better, a square) to define the area for the 3D model. An Insert 3D dialog box appears.
- In the Insert 3D dialog box, browse to select your myMol.u3d file. Check Show Advanced Options to set the initial properties.
- Adobe help for this procedure.

Viewing the result

Check the 3D display in a PDF viewer application. Note that not all viewers support this kind of 3D content.
- The pdf viewers implemented internally in web browsers do not currently support 3D objects and will just display a static image.
- Adobe Acrobat Pro and the free Adobe Reader support 3D objects.
- PDF-XChange Editor supports 3D objects.
- Recent versions of Foxit PDF Reader support 3D objects. Display of 3D objects may be disabled by default. You may enable it either by trusting the document or by setting: File > Preferences > 3D > Enable the playing of 3D content.
In Android devices you may use '3D PDF Viewer' or possibly other apps (search the Google Play store).
In iOS devices you may use '3D PDF Viewer' (search the App Store) or possibly other apps. This may also be run in a Mac computer.

Sample documents

These have been created following the above procedure

Note the model will not display as 3D and interactive if you view it inside the web browser; you need to download the file and open it in a compatible PDF viewer.

Older reference

This old content may or not be currently useful, but it is kept for the record at File_formats/3D_PDF/Legacy

Contributors

AngelHerraez, Vdlee

@@ Line 1: / Line 1: @@
 = 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''' (at least free in Windows; solutions for the Mac need more investigation to confirm).
-== Installations ==
+=== Downloads ===
-=== Jmol ===
+* ''Windows'' ''and MacOS'': download the '''graphic user interface version of IDTFConverter''' from [https://jmol.sourceforge.net/download/ the Jmol website]:
-You need at least version 12.0.RC26 to do this.
+** ''Windows'': download the {{file|IDTF_U3D_Converter.zip}}, unpack the zip file and put the single {{file|IDTF_U3D_Converter.exe}} file wherever you want in your local disk. If you find it convenient, create a shortcut for it in the desktop or the Start menu.
+** ''MacOS'': choose and download the app suitable for your system:
+*** {{file|IDTF_U3D_Converter_Intel.zip}} if your computer is based on an [https://en.wikipedia.org/wiki/MacBook_Pro_(Intel-based) Intel processor]. Unpack the zip file to obtain the executable file, {{file|IDTF_U3D_Converter.app}}
+*** {{file|IDTF_U3D_Converter_Silicon.zip}} if your computer is based on a [https://en.wikipedia.org/wiki/Apple_silicon Silicon processor] (usually ARM). Unpack the zip file to obtain the executable file, {{file|IDTF_U3D_Converter.app}}
-=== IDTF to U3D ===
+=== Create the IDTF file ===
-(See also descriptions and comments for Jmol output to [[File_formats/3D_Objects#IDTF|IDTF]] and [[File_formats/3D_Objects#U3D|U3D]] formats.)
-* ''Windows'' installation of IDTFConverter
+# Get a current version of '''Jmol''' application. Open your molecule; display it in the desired orientation and style.
-# Download and unzip http://www.iaas.msu.ru/tmp/u3d/u3dIntelWin.zip into, perhaps, {{file|c:\idtf\}}
+#* ''Suggestion: make the Jmol window square'', using <code>top menu > Display > Resize</code> and entering two equal numbers. The result will look better if you insert it later into a square box within the pdf.
-# Create a simple command file {{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 {{file|u3d.bat}} file must contain this text:
+#* ''Note:'' you can also do it with JSmol embedded in some webpage. Generation of the idtf file may take longer, though, if the model is complex.
-:: <code>c:\idtf\idtfconverter.exe -input %1.idtf -output %1.u3d</code>
+# If the export to IDTF option has been implemented in the menu:
+#* Top menu bar > <code>File > Export > Export to IDTF</code>
+#* Pop-up context menu > <code>File > Export > Export IDTF 3D model</code>
+# Otherwise, open the console and enter <code>write myMol.idtf</code>
+# Two files will be created: {{file|myMol.idtf}} and {{file|myMol.idtf.tex}}. For the current method, you may discard the <code>.tex</code> file.
-* ''MacOS and Linux'' installation of IDTFConverter
+=== Create the U3D file ===
-# See [[File_formats/3D_Objects#IDTF|IDTF]] for instructions on getting the converter.
-# Create a command file similarly to the one described for Windows.
-=== LaTeX to PDF ===
+* Open the '''IDTF_U3D_Converter''' program or app, browse to load your {{file|.idtf}} file, choose the output folder and click on "Convert". The output will have the same filename as the input, with extension {{file|.u3d}}
-There are several '''pdfLatex''' software, like '''[http://www.tug.org/tetex/ teTeX]''' (Unix; discontinued in 2006), '''[http://miktex.org/ MiKTeX]''' (Windows), '''[http://www.tug.org/texlive/ TeX Live]''' (Unix, Linux, Windows), '''[http://www.tug.org/mactex/2009/ MacTeX]'''...
+[[File:IDTF_U3D_Converter.png|thumb|center|x200px]]
-* Installation of MiKTeX (Windows)
+=== Prepare your PDF document ===
-# Download and install '''MiKTeX "basic"''' from http://miktex.org/
-# Do an update (menu <code>Programs > MiKTeX > Maintenance > Update</code>)
-# Download the '''movie15''' package (menu <code>Programs > MikTex > Maintenance > Package Manager</code>)
-== Creating the document ==
+# Use your preferred program (word processor, presentation, ...) to create a document with text and images, leaving square space(s) where you will later insert the 3D molecular models, and export to pdf format.
-. Within Jmol script console: <code>write c:/temp/xxx.idtf</code>
+#* If your application cannot export to PDF directly, you may use a virtual PDF printer like [https://www.pdfforge.org/ PDFforge PDF Creator] or [https://www.pdf-xchange.com/product/pdf-xchange-lite PDF-XChange Lite Printer] (both available for free).
-: or from the application's pop-up menu: <code>File > Export IDTF 3D model</code> (a dialog prompts for destination folder and filename).
+# To insert the 3D models you need a pdf editor that is compatible with the 3D-PDF standard. Examples: Adobe Acrobat Pro and  [https://www.pdf-xchange.com/product/pdf-xchange-editor PDF-XChange Editor] (Windows-only, free or paid version)
-: Either of those will create two files: {{file|xxx.idtf}} and {{file|xxx.idtf.tex}}
+# In PDF-XChange Editor: open the previous PDF, find the place where your left blank space. To insert a ''3D annotation'' there:
+#* If you are using the Ribbon interface: <code>Comment > Add 3D</code>
+#* If you are using the classical Toolbar interface: <code>Tools > Media tools > Add or edit 3D annotations</code>
+#* Draw the rectangle area with the mouse. ''Suggestion:'' draw a square by holding the Shift key while dragging to define the area.
+#* In <code>3D Artwork</code>, select your {{file|myMol.u3d}} file.
+#* Choose among any other display options offered (like activation of the content, border and background color)
+#* Accept and save the file.
+# In Adobe Acrobat Pro: open the previous PDF, find the place where your left a blank space. To insert ''3D media'' there:
+#* From the upper left of the screen, select <code>All tools > Add rich media > 3D media</code>.
+#* Drag a rectangle (better, a square) to define the area for the 3D model. An Insert 3D dialog box appears.
+#* In the <code>Insert 3D</code> dialog box, browse to select your {{file|myMol.u3d}} file. Check <code>Show Advanced Options</code> to set the initial properties.
+#* [https://helpx.adobe.com/acrobat/using/adding-3d-models-pdfs-acrobat.html Adobe help] for this procedure.
-. At the system command line or terminal, call the {{file|u3d.bat}} file (Windows), or equivalent MacOS or Linux command file, to convert the {{file|.idtf}} to {{file|.u3d}} format:
+=== Viewing the result ===
-: <code>u3d c:\temp\xxx</code>
+* Check the 3D display in a PDF viewer application. Note that not all viewers support this kind of 3D content.
+** The pdf viewers implemented internally in web browsers '''do not''' currently support 3D objects and will just display a static image.
-. Run the '''TeXworks''' program --included in MiKTeX-- and open in it your {{file|xxx.idtf.tex}}.
+** Adobe Acrobat Pro and the free Adobe Reader support 3D objects.
+** PDF-XChange Editor supports 3D objects.
-. Click menu item <code>Typeset > Typeset</code>, or click on the green 'play'-like button (leftmost in the toolbar).
+** Recent versions of [https://www.foxit.com/pdf-reader/ Foxit PDF Reader] support 3D objects. Display of 3D objects may be disabled by default. You may enable it either by '''trusting''' the document or by setting: ''File > Preferences > 3D > Enable the playing of 3D content''.
-: When processing ends, you will see a blank document in a new TeXworks window, because MiKTeX can't display the model, but {{file|xxx.idtf.pdf}} should have been created.
+* In Android devices you may use '3D PDF Viewer' or possibly other apps (search the Google Play store).
+* In iOS devices you may use '3D PDF Viewer' (search the App Store) or possibly other apps. This may also be run in a Mac computer.
-. Open the {{file|.pdf}} file using Adobe Reader v. 7 or later.
-: If you don't see the model in its panel inside the document, right-click on it and choose <code>Partial options > Fit visible</code>
-=== 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 [http://www.tracker-software.com/product/pdf-xchange-viewer PDF-XChange Viewer], allow you to add text and images onto the generated 3D PDF.
 == Sample documents ==
-(Text in these documents has been added externally to the process descrbed here.)
+These have been created following the above procedure
+* [[:File:Cys_3D.pdf|Cysteine]]
-* 3D PDF with an [http://biomodel.uah.es/Jmol/3d-pdf/dan002.pdf organic molecule], ball and stick.
+* [[:File:Ala_3D.pdf|Alanine]]
-: Model {{file|.hin}} 5 kB; {{file|.idtf}} 121 kB; {{file|.u3d}} 47 kB; {{file|.pdf}} 18 kB.
+* [[:File:Factor_Xa.pdf|Coagulation Factor Xa]]
-* 3D PDF with a small protein, [http://chemapps.stolaf.edu/jmol/docs/examples-11/pdf/test1.idtf.pdf crambin] (1crn.pdb), in cartoon rendering.
+Note the model will not display as 3D and interactive if you view it inside the web browser; you need to download the file and open it in a compatible PDF viewer.
-* 3D PDF with a polyhedra rendering of [http://chemapps.stolaf.edu/jmol/docs/examples-11/pdf/quartzPolyhedra.idtf.pdf quartz].
-* 3D PDF with a carbon [http://biomodel.uah.es/Jmol/3d-pdf/nanotube.pdf nanotube], ball and stick and molecular surface.
-: Model {{file|.hin}} 16 kB; {{file|.idtf}} 1800 kB; {{file|.u3d}} 182 kB; {{file|.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).
-== 3D PDF Editors ==
+= Older reference =
-* Adobe Acrobat Pro (proprietary, commercial).
+This old content may or not be currently useful, but it is kept for the record at [[File_formats/3D_PDF/Legacy]]

Difference between revisions of "File formats/3D PDF"

Latest revision as of 12:30, 26 March 2026

Contents

PDF documents with integrated 3D interactive models

Easy procedure

Downloads

Create the IDTF file

Create the U3D file

Prepare your PDF document

Viewing the result

Sample documents

Older reference

Contributors

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