File formats/3D PDF - Revision history

AngelHerraez at 12:30, 26 March 2026

2026-03-26T12:30:29Z

Show changes

AngelHerraez: /* Sample documents */

2026-03-26T12:15:00Z

‎Sample documents

AngelHerraez: /* Create the U3D file */

2026-03-25T20:52:07Z

‎Create the U3D file

AngelHerraez: update and improve info, also for Mac

2026-03-25T11:26:04Z

update and improve info, also for Mac

AngelHerraez: /* Easy procedure */

2026-02-28T15:55:56Z

‎Easy procedure

AngelHerraez: /* Easy procedure */

2026-02-28T11:31:26Z

‎Easy procedure

AngelHerraez: adding information about using GUI version of IDTFConverter

2026-02-25T17:35:45Z

adding information about using GUI version of IDTFConverter

AngelHerraez: /* References */

2026-02-20T19:45:45Z

‎References

AngelHerraez: /* Sample documents */

2024-04-25T15:31:43Z

‎Sample documents

AngelHerraez: /* Easy procedure */ more details

2024-04-23T14:38:49Z

‎Easy procedure: more details

@@ Line 53: / Line 53: @@
 * [[:File:Cys_3D.pdf|Cysteine]]
 * [[:File:Ala_3D.pdf|Alanine]]
 = Older reference =

← Older revision		Revision as of 20:52, 25 March 2026
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	* 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}}		* 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}}
		+	[[File:IDTF_U3D_Converter.png\|thumb\|center\|x200px]]

	=== Prepare your PDF document ===		=== Prepare your PDF document ===

@@ Line 1: / Line 1: @@
 = PDF documents with integrated 3D interactive models =
 == Easy procedure ==
-'''Only in Windows'''.
+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).
-(This is a brief description; if needed, extra information may be found in the next section below)
+=== Downloads ===
-# Create a '''PDF document''' with the text and images from your preferred application (e.g. Word, 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 [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).
+=== Create the IDTF file ===
-# Download the '''graphic user interface version of IDTFConverter''' from [{{SVN Trunk}}IDTF_U3D_converter/ Jmol SVN repository]. Unpack the zip file and put the single <code>IDTF_U3D_Converter.exe</code> file wherever you want in your local disk. Create a shortcut for it in the desktop if you find it more convenient.
-# Download and install [https://www.pdf-xchange.com/product/pdf-xchange-editor '''PDF-XChange Editor'''] (free version); you need 8.0.332 at least (26 Aug. 2019)
+# Get a current version of '''Jmol''' application. Open your molecule; display it in the desired orientation and style.
-# Get a current version of '''Jmol'''. Open your molecule; display it in the desired orientation and style.
+#* ''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.
-#* ''Suggestion: make the Jmol window square'', using <code>top menu > Display > Resize</code> and entering two equal numbers.
+#* ''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.
-#* (''Note: export image file may be unnecessary, read item 7 below'')
+# If the export to IDTF option has been implemented in the menu:
-#* Export to an image file (that will be used as ''poster image'' to be displayed in the pdf until the 3D is enabled) using either
+#* Top menu bar > <code>File > Export > Export to IDTF</code>
-#** <code>top menu > File > Export > Export image</code> and selecting <code>Image type: PNG > Save</code>
+#* Pop-up context menu > <code>File > Export > Export IDTF 3D model</code>
-#** or <code>pop-up menu > File > Export > Export PNG image > Save</code>
+# Otherwise, open the console and enter <code>write myMol.idtf</code>
-#** ''Note:'' Make sure to include the <code>.png</code> file extension with the chosen filename (Jmol will not add it)
+# 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.
-#* Using the console, export the model to IDTF format: <code>write myMol.idtf</code>
-# Two files have been created: {{file|myMol.idtf}} and {{file|myMol.idtf.tex}}. For this method, you only need the first one.
+=== Create the U3D file ===
-# Run the <code>IDTF_U3D_Converter.exe</code>. In the application, find and select your IDTF file, then select the folder where you want to save the output file. Click on [Convert] and that will save the file to the chosen folder, with the same original filename and extension <code>.u3d</code>
-# Open the previous PDF file into PDF-XChange Editor. Find the place where your left blank space. To insert a ''3D annotation'' there:
+* 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}}
 #* 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.
+#* Draw the rectangle area with the mouse. ''Suggestion:'' draw a square by holding the Shift key while dragging to define the area.
-#* <code>3D Artwork</code>: select your {{file|myMol.u3d}} file.
+#* In <code>3D Artwork</code>, select your {{file|myMol.u3d}} file.
-#* (''Note: the following seems to be not necessary in the currenty version, the image is taken as a snapshot from the u3d file'')
+#* Choose among any other display options offered (like activation of the content, border and background color)
 #* Accept and save the file.
-# Check the 3D display in a PDF viewer application. Note that not all viewers support this kind of 3D content. At least, Adobe Reader and PDF-XChange Editor support 3D objects.
+# In Adobe Acrobat Pro: open the previous PDF, find the place where your left a blank space. To insert ''3D media'' there:
 == Sample documents ==

@@ 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''' under '''Windows'''.
+'''free software'''.
 (This is a brief description; if needed, extra information may be found in the next section below)
@@ Line 10: / Line 11: @@
 # Download and install [https://www.pdf-xchange.com/product/pdf-xchange-editor '''PDF-XChange Editor'''] (free version); you need 8.0.332 at least (26 Aug. 2019)
 # Get a current version of '''Jmol'''. Open your molecule; display it in the desired orientation and style.
-#* ''Suggestion: make the Jmol window square'', using <code>top menu > Display > Resize</code> and enterung two equal numbers.
+#* ''Suggestion: make the Jmol window square'', using <code>top menu > Display > Resize</code> and entering two equal numbers.
 #* Export to an image file (that will be used as ''poster image'' to be displayed in the pdf until the 3D is enabled) using either
 #** <code>top menu > File > Export > Export image</code> and selecting <code>Image type: PNG > Save</code>

@@ Line 6: / Line 6: @@
 (This is a brief description; if needed, extra information may be found in the next section below)
-# Create a '''PDF document''' with the text and images from your preferred application (e.g. Word, 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 [https://www.pdfforge.org/ PDFforge PDF Creator] or [https://www.tracker-software.com/product/pdf-xchange-lite PDF-XChange Lite Printer] (both available for free).
+# Create a '''PDF document''' with the text and images from your preferred application (e.g. Word, 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 [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).
-# Download the '''graphic user interface version of IDTFConverter''' from ...(to be filled in). Unpack the zip file and put the single <code>IDTF_U3D_Converter.exe</code> file wherever you want in your local disk. Create a shortcut for it in the desktop if you find it more convenient.
+# Download the '''graphic user interface version of IDTFConverter''' from [{{SVN Trunk}}IDTF_U3D_converter/ Jmol SVN repository]. Unpack the zip file and put the single <code>IDTF_U3D_Converter.exe</code> file wherever you want in your local disk. Create a shortcut for it in the desktop if you find it more convenient.
 # Download and install [https://www.pdf-xchange.com/product/pdf-xchange-editor '''PDF-XChange Editor'''] (free version); you need 8.0.332 at least (26 Aug. 2019)
 # Get a current version of '''Jmol'''. Open your molecule; display it in the desired orientation and style.
@@ Line 23: / Line 23: @@
 #: Draw the rectangle area with the mouse. ''Suggestion:'' draw a square by holding the Shift key while dragging to define the area.
 #* <code>3D Artwork</code>: select your {{file|myMol.u3d}} file.
-#* <code>Appearance > Poster > Create poster from file</code> and select the png file you previously saved from Jmol. ''Sometimes this is not necessary and the image will be made from the u3d file (not verified)''
+#* (''Note: the following seems to be not necessary in the currenty version, the image is taken as a snapshot from the u3d file'')
 #* Choose among any other options offered for display (like border and background color)
 #* Accept and save the file.

@@ Line 64: / Line 64: @@
 #: You need to extract the contents of {{file|u3dIntelWin/}}: several files and the {{file|Plugins}} folder; the {{file|doc/}} and {{file|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 {{file|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 ===

@@ Line 9: / Line 9: @@
 # Download and install '''IDTFConverter'''; create a {{file|u3d.bat}} file for convenience (see below for addresses and details).
 # Download and install [https://www.tracker-software.com/product/pdf-xchange-editor '''PDF-XChange Editor'''] (free version); you need 8.0.332 at least (26 Aug. 2019)
-# 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: <code>write myMol.idtf</code>
+# Get a current version of '''Jmol'''. Open your molecule; display it in the desired orientation and style.
 # Two files have been created: {{file|myMol.idtf}} and {{file|myMol.idtf.tex}}. Copy them to the folder where you have IDTFConverter, open the command line there and run the conversion: <code>u3d.bat myMol</code>.  That will create a {{file|myMol.u3d}}
 # 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: <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 and pick your {{file|myMol.u3d}} file. Choose among the options offered for display, accept and save the file.
+#: Draw the rectangle area with the mouse. ''Suggestion:'' draw a square by holding the Shift key while dragging to define the area.
-# Check the 3D display in a PDF viewer application (note that only Adobe Reader and PDF-XChange Editor support this kind of 3D content)
+#* <code>3D Artwork</code>: select your {{file|myMol.u3d}} file.
 == Sample documents ==