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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 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)
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.