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===<div style="background-color:#efeddf; 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 style="background-color:#efeddf; margin-top:0px;border-bottom: 1px dotted #999999; padding-top:3px;font-weight:normal;">'''Case 1:''' Overall fold / domain level (Fig. 2; ≥ novice/intermediate) | ||
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Illustration of the overall fold of carbonic anhydrase, CsoS3, from Halothiobacillus neapolitanus.(PDB ID 2G13). The three domains that compose this enzyme are distinguished by coloring each domain separately (blue, yellow, red). The orientation was chosen to feature the location of the active site (outlined by side chains and zinc ion), and to show the two-fold symmetry relationship between the active domain (yellow) and homologous but defunct domain (red). SSEs are labeled directly on the individual SSEs. Domain labels are colored to correspond to the domains they are labeling. Labels in the active site are given an “outer glow” to make them legible in a region of the figure that is dense in detail. Depth is conveyed by use of fog, veiling less important structural features in the back of the enzyme. | Illustration of the overall fold of carbonic anhydrase, CsoS3, from Halothiobacillus neapolitanus.(PDB ID 2G13). The three domains that compose this enzyme are distinguished by coloring each domain separately (blue, yellow, red). The orientation was chosen to feature the location of the active site (outlined by side chains and zinc ion), and to show the two-fold symmetry relationship between the active domain (yellow) and homologous but defunct domain (red). SSEs are labeled directly on the individual SSEs. Domain labels are colored to correspond to the domains they are labeling. Labels in the active site are given an “outer glow” to make them legible in a region of the figure that is dense in detail. Depth is conveyed by use of fog, veiling less important structural features in the back of the enzyme. | ||
===<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>=== | ===<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>=== | ||
Revision as of 18:59, 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.
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Illustration of the overall fold of carbonic anhydrase, CsoS3, from Halothiobacillus neapolitanus.(PDB ID 2G13). The three domains that compose this enzyme are distinguished by coloring each domain separately (blue, yellow, red). The orientation was chosen to feature the location of the active site (outlined by side chains and zinc ion), and to show the two-fold symmetry relationship between the active domain (yellow) and homologous but defunct domain (red). SSEs are labeled directly on the individual SSEs. Domain labels are colored to correspond to the domains they are labeling. Labels in the active site are given an “outer glow” to make them legible in a region of the figure that is dense in detail. Depth is conveyed by use of fog, veiling less important structural features in the back of the enzyme.
Case 2: Ligand-binding sites (Fig. 3; ≥ novice/intermediate)
Case 3: Structure alignment(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 (≥ intermediate/advanced)
See the Animations section below.
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.