User:David Canner/Sandbox good: Difference between revisions
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This is a list of tips and tricks to develop effective scenes for your pages. | This is a list of tips and tricks to develop effective scenes for your pages. | ||
==Scene Transitions== | ==Scene Transitions== | ||
===Smooth Transitions=== | ===Smooth Transitions=== | ||
<StructureSection load='1dq8' size='500' side='right' scene='HMG-CoA_Reductase/1dq8_starting_scene/1' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])'> | <StructureSection load='1dq8' size='500' side='right' scene='HMG-CoA_Reductase/1dq8_starting_scene/1' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])'> | ||
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]]: | Example from the page [[HMG-CoA Reductase]]: | ||
The HMG binding pocket is the site of catalysis in HMGR. <scene name='HMG-CoA_Reductase/1dqa_cis_loop2/2'> The “cis-loop” that bends over the top of HMG </scene> is a critical structural element of this binding site. Residues <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> and are positioned in the active site as is <scene name='HMG-CoA_Reductase/1dqa_k691/2'>K691 which is only 2.7 angstroms from the HMG O2 carbonyl oxygen</scene>. 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 <scene name='HMG-CoA_Reductase/1dqa_h866/2'>H866, which is within hydrogen bonding distance of the thiol group</scene>. It is then believed that the close proximity of <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> increases the pKA of E559, allowing it to be a proton donor for the reduction of mevaldehyde into mevalonate.<br /> | The HMG binding pocket is the site of catalysis in HMGR. <scene name='HMG-CoA_Reductase/1dqa_cis_loop2/2'> The “cis-loop” that bends over the top of HMG </scene> is a critical structural element of this binding site. Residues <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> and are positioned in the active site as is <scene name='HMG-CoA_Reductase/1dqa_k691/2'>K691 which is only 2.7 angstroms from the HMG O2 carbonyl oxygen</scene>. 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 <scene name='HMG-CoA_Reductase/1dqa_h866/2'>H866, which is within hydrogen bonding distance of the thiol group</scene>. It is then believed that the close proximity of <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> increases the pKA of E559, allowing it to be a proton donor for the reduction of mevaldehyde into mevalonate.<br /> | ||
Revision as of 11:34, 21 November 2010
How to make excellent scenes:
This is a list of tips and tricks to develop effective scenes for your pages.
Scene TransitionsScene Transitions
Smooth TransitionsSmooth 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 . Etc… |
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