PDB files

“Browse” will allow you to upload a file from your computer

“use PDB id” will fetch an entry from the PDB archive

“Project name” allows you to control the names of files that are generated

“Advanced” options allow display of waters and/or hydrogens (which are omitted by default), as well as access to shadowing and outlining parameters

Scale Factor

“Pixel per Angstrom” is the scale factor used to create the illustration


“Style” provides several default display styles. These include:

  • Protein/DNA–proteins in blue, DNA/RNA in red, and heteroatoms in green
  • Entity/Chain–uses IWantHue to assign different colors to subunits
  • Atomic–modified atomic coloring, with charged oxygen/nitrogen in saturated red/blue, and polar oxygen/nitrogen in pastel colors
  • CPK–traditional atomic colors
  • One color–user defined color used for all atoms
  • One color range–user defined color, with carbon atoms slightly lighter than other atoms
  • Coarse–large spheres used for alpha carbons and two atoms in nucleic acids, using a protein/DNA coloring scheme
  • Generic–just outlines, for use in CellPAINT
  • Advanced–prototype method for user-defined selections, each with a given color. The three boxes are atom names, residue names, and chain ID.

Customizing Scripts

“PREVIEW INPUT TXT” displays the Illustrate script in an editable window.

If you make manual changes, click on the “Use Input Script” box to use it for illustration.

Note: if you use this script, subsequent changes in the NGL window will not be applied.

Additional buttons will clear this script and allow uploading of external scripts.

Creating the Illustration

“Assembly” and “ModelID” buttons allow choice of different types of biological assemblies and different models. When you read in a PDB file, checkboxes will also appear for the different chains in the PDB entry–make sure that at least one is checked. The “Selection” box shows the current selection.

“ILLUSTRATE” launches the Illustrate program. The time to calculate the image will be proportional to the number of atoms and also the scale factor.

The website is designed to allow quick access to several useful representations, and options for customizing representations as you become more familiar with the method.

To get started:

1) type a PDB id in the “use PDB id” box

2) choose one of the options in “Style”

3) orient the molecule in the NGL window

4) click on “ILLUSTRATE”

5) when the image appears, you can save it by right-click on the image


Biological molecules, and the ways that scientists study them, are immensely diverse and complex, so it is difficult to find defaults that work for everything. A few places that you might encounter problems include:

1) very large molecules may not fit within the maximum image size of 3000X3000 pixels. If this happens, try a smaller “Pixel per Angstrom” scale size.

2) HETATMs are used in several ways in PDB entries, including free ligands and substrates and modified amino acids and nucleotides in chains. You may have to tweak the script manually to get the results you want.