Supplementary material 2:

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

This text is a supplementto:

Grasping molecular structures through publication-integrated 3D models

Pravin Kumar1,*, Alexander Ziegler 2,*, Julian Ziegler1,3, Barbara Uchanska-Ziegler1and Andreas Ziegler1

1 Institut für Immungenetik, Charité –Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73,14195 Berlin, Germany

2 Institut für Biologie, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany

3 Current address: Meister-Francke-Strasse 8, 22309 Hamburg, Germany

Trends in Biochemical Sciences, Volume 33, Issue 9, September 2008

Figure 1:

The following is a guide for generating 3D models from a PDB file using a licensed version of PyMOL together with Adobe 3D Reviewer and Adobe Acrobat 9 Pro Extended. Itisalso available online at The goal of the exercise is to show you how to reproduce the image in Figure 1as an interactive 3D model in a PDF file, thus teaching you the basics of the process.

PART 1: Model creation using PyMOL

Step 1:The3D models of the structures in Figure 1 are originally generated using the following script in PyMOL,using the file 1UXS.pdb downloaded from the Protein DataBank.

Note, if you are unfamiliar with the syntax used in PyMOL, it is possible to use the graphical user-interface (GUI) of the software to manually load the PDB file, configure the display of the molecule and create the image from it.

Script 1:

load 1UXS.pdb

bg_color white

hide

select groove, resi 1-180 and chain a

select peptide, resi 1-9 and chain c

show cartoon, groove

color white, groove

show stick, chain c

set_view (\

-0.912446856, -0.163690791, -0.375027299,\

-0.052661002, 0.955854416, -0.289084166,\

0.405792415, -0.244024336, -0.880786359,\

0.000007013, 0.000006229, -147.386962891,\

5.790267467, 0.459395200, 11.122777939,\

96.323867798, 198.451461792, 0.000000000 )

ray

save Fig1.png

Step 2: Divide the model into individual components and export their coordinates as VRML2 models. You can use the following PyMOL script.

Script 2:

hide everything

show stick, peptide

save peptide.wrl

Alternatively you can use the GUI to modify the display settings and use the “Save Image As …VRML2” File menu option (Figure 2).

Figure 2:

Similarly the second component of the model, the peptide binding groove, can also be exported as a VRML2 model using the following script (or by using the GUI, Figure 3).

Script 3:

hide everything

show cartoon, groove

save groove.wrl

Figure 3:

Part II: Figure Creation using Adobe Acrobat 9 Professional Extended

Step 3: Open Adobe 3D Reviewer,which is a part of the Adobe Acrobat 9 Professional Extended software suite. Click the “Open” icon and select ALLthe components of your 3D model (which are all in .wrl format) using the “Ctrl” key, then press “Open” (Figure4) to import them into Adobe 3D Reviewer.

Figure 4:

Options to alter the background colour, light settingsetc. appear on right clicking on the screen (Figure5).

Note, we have found that changing the ‘Level of Detail’ setting does not appear to have any effect for our models or on the final file-size of the PDF – we suggest ignoring this option.

Figure 5:

Note: (Not shown here) if you click an object in your model to select it, and then right-click the selection, you will be presented with a contextual menu from which you can select a‘Properties’ option. In the dialogue that appears, you can modify the colour of your selected object, which enables you to colour code e.g. different subunits in your final figure.

Export the model as a .u3d file (Figure6). Note, you must change the export settings by clicking the Options button that appears at the bottom left of the Export dialogue if you wish to create a PDF that is compatible with version 7.1 of Adobe Reader or Acrobat. To do so, choose‘ECMA 1 (7.0 compatible)’ for the export format (the default is ECMA 3 which is only compatible with version 8 and higher).

Figure 6:

Step 3: Now open Adobe Acrobat 9 Pro Extended. Click the “Open” icon, select the folder in which the Adobe 3D Reviewer file was created, opt to ‘Show all files’ (the default is PDFs only) and choose the saved .u3d model to be opened (Figure7). Click OK on the dialogue that is displayed to convert the file.

Note: if compatibility with version 7.1 of Adobe Reader is required, it is important that you do not change any of the conversion settings available in this dialogue from their defaults.

Figure 7:

In our example, the opened, converted model looks like this (Figure8).

Figure 8:

Right click and select “Properties” (Figure9).

Figure 9:

Set the options in the “Launch Settings” tab. If you want to set a specific static 2D image for your interactive model (such as a 2D Figure for an article) click “Create poster from file” (Figure 10), and choose e.g. the Fig1.png that was created in PyMOL earlier.If you skip this step, an image will be created for you from the default view of the 3D model itself.

Figure 10:

You can change the background color, light settings etc. under the “3D” tab of the same dialogue (Figure 11).

Note: also under this tab are options to have the model tree and toolbar display automatically whenever the interactive 3D model is opened by a reader. At this point it can also be beneficial to opt to ‘Add Default Views’ to your model tree (i.e. views from Top, Left, Right, Bottom, etc.), which will make it easier to perform the stage illustrated in Figure 13 further below.

Figure 11:

On clicking “OK” you will see the static 2D image you have chosen (Figure 12). Click anywhere on the image to activate the 3D display of the molecule.

Figure 12:

Click on the “Model tree” icon to display the model tree pane (Figure13). This will permit you to add predetermined viewsfor the reader (if you added thedefault views above, you can use these as the basis for your own views e.g. by zooming in on them, etc and renaming them).

Figure 13:

To add further views, after generating a new display for your molecule (by zooming, dragging and rotating with the mouse) click on the “Create View” icon to embed this view in the model tree (Figure14).

Figure 14:

Rename the designation of the new view to your liking by double clicking the “NewView” title (Figures. 15 and 16).

Figure 15:

Figure 16:

From the listing in the model tree, choose a “Default view” that will be seen when the 3D mode is activated by the reader (Figure17).

Figure 17:

Save the file as a PDF and exit Adobe Acrobat 9 Pro Extended.

Step 4: You will now be able to open the PDF that you have just created in Adobe Reader or Adobe Acrobat 7.1 or higher and view the 3D model.