User:David Canner/Sandbox good
From Proteopedia
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===Smooth Transitions=== | ===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.==== | ====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 [[ | + | =====Example from the page [[The Structure of PI3K]]: ===== |
| - | <center><scene name=' | + | <center><scene name='User:David_Canner/Sandbox_P/Nsh2_full/1'>Initial Scene (Reset)</scene> </center> |
| - | + | Although no <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>crystal structure of PI3K</scene> with bound substate analog has been solved, a model for PIP2 phosphorylation has been developed and is generally supported. In this model, the headgroup of PIP2 is <scene name='User:David_Canner/Sandbox_P/Catalytic_cavity/2'>positioned in a cavity</scene> between the <scene name='User:David_Canner/Sandbox_P/Catalytic_site/1'>C-terminal helix 12 of the kinase domain, the “activation” loop, and the “catalytic” loop</scene>. This puts the 5-phosphate of PIP2 near Lys 973 and the <scene name='User:David_Canner/Sandbox_P/Catalytic_site_atp_lys/1'>I-phosphate of ATP near Lys 807 and Lys 808</scene>. The <scene name='User:David_Canner/Sandbox_P/Catalytic_site_pip2/1'>basic residues Arg 947</scene> and Lys 973 can bind the 4-Phosphate of PIP2 and help provide the Class I PI3Ks with their specificity for PIP2. Once PIP2 and ATP are bound, it is believed <scene name='User:David_Canner/Sandbox_P/Catalytic_site_his/1'>His 948 rotates to interact with PIP2</scene>, deprotonating it at the C-3 Hydroxyl position creating a nucleophile. This nucleophile subsequently attacks the gamma phosphate of ATP producing PIP3. | |
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====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==== | ====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]] ===== | =====Example from the page [[The Structure of PI3K]] ===== | ||
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<center><scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset)</scene> </center> | <center><scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset)</scene> </center> | ||
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 <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>within the kinase domain</scene> of PI3Kγ and how various inhibitors prevent this interaction helps elucidate ways to develop effective, selective inhibitors. See p110γ bound to <scene name='User:David_Canner/Sandbox_P/Inhibitor_atp/5'>ATP</scene> ([[1e8x]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_wortmannin/7'>Wortmannin</scene> ([[1e7u]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_ly294002/2'>LY294002</scene> ([[1e7v]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_quer/2'>Quercetin</scene> ([[1e8w]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_staur/1'>Staurosporine</scene> ([[1e8z]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_myrice/1'>Myricetin</scene> ([[1e90]]). | 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 <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>within the kinase domain</scene> of PI3Kγ and how various inhibitors prevent this interaction helps elucidate ways to develop effective, selective inhibitors. See p110γ bound to <scene name='User:David_Canner/Sandbox_P/Inhibitor_atp/5'>ATP</scene> ([[1e8x]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_wortmannin/7'>Wortmannin</scene> ([[1e7u]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_ly294002/2'>LY294002</scene> ([[1e7v]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_quer/2'>Quercetin</scene> ([[1e8w]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_staur/1'>Staurosporine</scene> ([[1e8z]]), <scene name='User:David_Canner/Sandbox_P/Inhibitor_myrice/1'>Myricetin</scene> ([[1e90]]). | ||
| + | ====Tip #6: Whenever possible, try to illustrate points using same .pdb file to avoid "choppy" scene transitions. If unavoidable, include "reorienting" scenes which provide a view of the entire protein.==== | ||
| + | =====Example from the page [[PI3K Activation, Inhibition, & Medical Implications]]:===== | ||
| + | <center><scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset)</scene> </center> | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
__NOTOC__ | __NOTOC__ | ||
Revision as of 10:23, 21 November 2010
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.
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