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How to Make Excellent Scenes

This is a list of tips and tricks to develop effective scenes for your pages. The scenes below were taken from the indicated pages.

Smooth Transitions

Tip #1: When developing a series of scenes illustrating related parts of a protein, use the “transition options” to create smooth transitions void of peculiar zoom-outs, etc.

Example from the page HMG-CoA Reductase:

The HMG binding pocket is the site of catalysis in HMGR. is a critical structural element of this binding site. Residues and are positioned in the active site as is . It is this K691 that likely stabilizes the negatively charged oxygen of the first mevaldyl-CoA intermediate. The mevaldyl CoA intermediate is subsequently converted to Mavaldehyde with added stabilization from . It is then believed that the close proximity of increases the pKA of E559, allowing it to be a proton donor for the reduction of mevaldehyde into mevalonate.

Compared with:

The HMG binding pocket is the site of catalysis in HMGR. is a critical structural element of this binding site. Residues and are positioned in the active site as is ...

Tip #2: It is best to establish a color scheme for all domains of interest and to stick with this color scheme throughout the analysis

Example from the page The Structure of PI3K

(residues 340-345) is anchored into Helix α11K of the (residues 1017-1024) nSH2 interacts with the through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong

Tip #3: Providing a wide view scene of an area of interest before zooming in provides context

Example from the page The Structure of PI3K

This loop in which contains the hotspots (residues 542-546) is located precisely where The salt bridge formed between like PDGFR, eliminating nSH2-mediated inhibition of p110α and activating the enzyme to phosphorylate PIP2 into PIP3.

Tip #4: When switching focus to a new domain, it is best to zoom out and orient the reader to the new domain of interest

Example from the page The Structure of PI3K:

(residues 340-345) is anchored into Helix α11K of the (residues 1017-1024) nSH2 interacts with the through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong

Tip #5: Eliminate the Scene transition when comparing different binding interactions for similar ligands

Example from the page PI3K Activation, Inhibition, & Medical Implications:

LY294002, a competitive inhibitor of ATP binding in the PI3K kinase domain, was first discovered by scientists at Eli Lilly. Quercetin, Myricetin & Staurosporine are natural compounds which broadly inhibit protein kinases. Understanding how ATP binds to the ATP binding site of PI3Kγ and how various inhibitors prevent this interaction helps elucidate ways to develop effective, selective inhibitors. See p110γ bound to (1e8x), (1e7u), (1e7v), (1e8w), (1e8z), (1e90).