Difference between revisions of "PLoS"
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| − | + | =<span style="font-family:Myriad-pro;">'''Biomolecular Graphics: In Principle and in Practice'''</span>= | |
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| + | =='''Overview, general notes'''== | ||
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| + | =='''Figures'''== | ||
| + | This section illustrates the figure-creation process, from initial conception → final multi-panel figure ready for publication. Organized as various "case studies" that are representative of the tasks typically faced by structural or computational biologists, this section provides several step-by-step examples. These examples are entirely self-contained, and the materials include everything from ''(i)'' raw, starting data (''e.g.'', PDB files) to ''(ii)'' actual, working PyMOL or Python scripts and ''(iii)'' final output image files. | ||
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| + | ===<div style="background-color:#eeecde; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 1:''' Overall fold / domain level (Fig. 2; ≥ novice/intermediate)</div>=== | ||
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| + | ===<div style="background-color:#eeecde; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 2:''' Ligand-binding sites (Fig. 3; ≥ novice/intermediate)</div>=== | ||
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| + | ===<div style="background-color:#eeecde; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 3:''' Structure comparison (Fig. 4; ≥ novice/intermediate)</div>=== | ||
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| + | ===<div style="background-color:#eeecde; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 4:''' Volumetric data (≥ intermediate)</div>=== | ||
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| + | ===<div style="background-color:#eeecde; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 5:''' Interfaces (Fig. 5; ≥ intermediate)</div>=== | ||
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| + | ===<div style="background-color:#eeecde; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 6:''' Higher-order structures (≥ intermediate/advanced)</div>=== | ||
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| + | ===<div style="background-color:#eeecde; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 7:''' Animations (see below ≥ intermediate/advanced)</div>=== | ||
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| + | ===<div style="background-color:#eeecde; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 8:''' Best-fit planes (Fig. 6; ≥ advanced)</div>=== | ||
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| + | =='''Animations'''== | ||
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| + | ===A classification scheme=== | ||
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| + | ===M<sub>s</sub>V<sub>s</sub>=== | ||
| + | These are just 'ordinary', static figures, as illustrated by the case studied above. | ||
| + | |||
| + | ===M<sub>s</sub>V<sub>d</sub>=== | ||
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| + | ===M<sub>d</sub>V<sub>s</sub>=== | ||
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| + | ===M<sub>d</sub>V<sub>d</sub>=== | ||
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| + | =='''Useful links'''== | ||
| + | |||
| + | ===PyMOL-related=== | ||
| + | ===Python-related=== | ||
| + | ===General MolVis=== | ||
Revision as of 16:56, 29 December 2009
Biomolecular Graphics: In Principle and in Practice
Overview, general notes
Figures
This section illustrates the figure-creation process, from initial conception → final multi-panel figure ready for publication. Organized as various "case studies" that are representative of the tasks typically faced by structural or computational biologists, this section provides several step-by-step examples. These examples are entirely self-contained, and the materials include everything from (i) raw, starting data (e.g., PDB files) to (ii) actual, working PyMOL or Python scripts and (iii) final output image files.
Case 1: Overall fold / domain level (Fig. 2; ≥ novice/intermediate)
Case 2: Ligand-binding sites (Fig. 3; ≥ novice/intermediate)
Case 3: Structure comparison (Fig. 4; ≥ novice/intermediate)
Case 4: Volumetric data (≥ intermediate)
Case 5: Interfaces (Fig. 5; ≥ intermediate)
Case 6: Higher-order structures (≥ intermediate/advanced)
Case 7: Animations (see below ≥ intermediate/advanced)
Case 8: Best-fit planes (Fig. 6; ≥ advanced)
Animations
A classification scheme
MsVs
These are just 'ordinary', static figures, as illustrated by the case studied above.