Images are shown at 1/3 size below. Use browser “save link as” to get PNG files of images 1200px wide with transparent background. It would be fairly easy to adjust colors, text labels, etc. if you like.

#15

• If you like ViewDock (as in the Screening Docked Molecules Image Gallery entry), here is a version to be placed over a white- or light-colored page: Besides the Image Gallery entry, there is also a feature highlight. The dialog image is not 1200px wide, it is the actual size of the dialog. Can use HTML to put a border (outline) around it, as is done here.
  
  
• Another nice possibility is a transparent-background version of the p53 Cancer Mutations Image Gallery entry: Two images, the same except for lighting style. See the Image Gallery entry for caption information.

#16

• Here's a large transparent-background version of the image from the Coloring by Conservation feature highlight: See the feature highlight for caption information. The corresponding sequence alignment is shown in the Multalign Viewer dialog image (not 1200px wide but the actual size of the dialog; as you can see by the horizontal scroll bar, only part of the alignment is visible). As above, HTML was used to put a border (outline) around it. You may not want the dialog image, I just included it for completeness and it shows some other neat features like the tree relationship of the sequences, obtained along with the (seed) sequence alignment from the PFAM database.
  
  
• I don't remember how I made the morphing feature highlight animated GIF (Chimera doesn't write that format), but you could use it “as is” if that would suffice. However, the Ball-and-socket motion movie in the Animation Gallery may be a nicer example of morphing anyway.
  • [YouTube]
  • [H.264 720x720]
  (H.264 format is what we uploaded to YouTube)
  
  
• There are many possibilities if you want to show a surface colored by electrostatic potential (ESP). One thing to consider is that you will already be showing surfaces colored by ESP in illustration #25. Putting that aside, however, in my opinion, the chaperonin image is “meh” with clear background because in the original Image Gallery entry, the back half recedes into darkness and then is cut off (but see it here if you want). Here are some alternatives:

  Two images in different styles of a protease domain (from PDB entry 3eeb) bound to a highly negatively charged small molecule, inositol hexakisphosphate (sticks). The molecular surface is colored red (negative) → white (neutral) → blue (positive) by Coulombic ESP, as in the Surface Properties image tutorial. You can see the markedly positive ESP in the binding pocket.

  
  
• The above shows electrostatic complementarity between a protein and a small molecule. The following shows it between two proteins:

  This shows the binding interface between porcine pancreatic trypsin (left) and a trypsin inhibitor from soybean (right). In the open position, each protein is rotated 90 degrees outward from the closed (bound) position shown on mouseover. Adapted from the Opened Interface image tutorial. Get full-sized (1200px wide) images from these links: [open] [closed] Animation open → closed → open: [H.264 400x250] [“still” of open position] [H.264 800x500] [“still” of open position] The motion in the animation is simply illustrative and not meant to be physically reasonable. The open position has the proteins slightly farther apart than in the image at left, to decrease their apparent intersection upon rotation to the closed position.

#17

• Again many possibilities, but how about a viral capsid? Here are two images of the hepatitis B viral capsid (made from PDB entry 2g33 using the Chimera Multiscale Models tool):

  Hepatitis B virus, capsid diameter approximately 420 Å. Each “blob” is a separate protein chain, with multiple copies of the same chain shown in the same color. In the righthand image, one copy of each protein is shown as ribbons instead of as a blob.

#18

#19

• [YouTube]
• [H.264 550x1000]

#20

#21

Note: as per journal instructions, should be accompanied by citation:

This research was originally published in Molecular & Cellular Proteomics. JH Morris, EC Meng, TE Ferrin. Computational Tools for the Interactive Exploration of Proteomic and Structural Data. Molecular & Cellular Proteomics. 2010; 9:1703-1715. © the American Society for Biochemistry and Molecular Biology.

#22

#23

You can see that the unknown (yellow) clusters more with the dipeptide epimerases (light green) than with the chloromuconate cycloisomerases (light red; this was the function suggested by the incorrect annotation of the unknown) or other families in the enolase superfamily. I thought the color key image from Cytoscape was annoying in terms of font, spacing, and ordering, so I reimplemented it in HTML (easier for your guys to use/modify if they want).

	color key image from Cytoscape:
	color key done in HTML:      unknown      dipeptide epimerase      chloromuconate cycloisomerase      muconate cycloisomerase (syn)      muconate cycloisomerase (anti)      N-succinylamino acid racemase 2      o-succinylbenzoate synthase      unclassified

#24

#25

Pocket surfaces colored by Coulombic ESP for the template structure 1tkkA (left) and a comparative model of MCA 1834 (right). The righthand surface looks a little blocky, but there were technical problems with making it smoother.