PLoS

Biomolecular Graphics: In Principle and in Practice

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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Case 1: Overall fold / domain level (Fig. 2; ≥ novice/intermediate)

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Stereo view of a protein fold

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.

#BEGIN PYMOL SCRIPT for left half of stereo image

#   antialias =1 smooths jagged edges, 0 turns it off
set antialias = 1

# Larger values of ambient make the image brighter
set ambient=0.3

# Larger values of direct eliminates shadows
set direct=1.0
set ribbon_radius =0.2

# cartoon_highlight_color will give a separate color to edges of secondary structural elements.
set cartoon_highlight_color =grey50

# ray_trace_mode=1 makes a black outline around the secondary structural elements
set ray_trace_mode=1

#   stick_radius -adjust thickness of atomic bonds
set stick_radius = 0.2

#   mesh_radius -to adjust thickness of electron density contours
set mesh_radius = 0.02

#   bg_color --set the background color
bg_color white

#   load pdb file and give it an object name
load csos3_18o_nobreak.pdb, csos3

#   hide nonbonded atoms (i.e. waters)
hide nonbonded

#   show cartoon ribbons
show cartoon

#   Hide the default line representation of atomic bonds
hide lines

#   Use standard helix, strand, and loop representations
#   other possibilities: cartoon loop, cartoon rect,
#   cartoon oval, and cartoon tube
set cartoon_tube_radius, 0.2

#   If you dont have secondary structure assignments
#   in the PDB header then get secondary structure assignments 
#   from dssp  http://swift.cmbi.kun.nl/gv/dssp/
#   Then convert assignments into a PDB header
#   http://structure.usc.edu/dssp2pdb/
#   If you want to define secondary structure manually, 
#   Use the following syntax 'S'=strand 'H'=helix
#   alter B/753:758/, ss='S'


#   Make fancy helices with ridge on the edges like
#   molscript does
#   1 is on.  0 is off.
set cartoon_fancy_helices=1
set cartoon_cylindrical_helices=0

#   Make the strands flat=1 or pass through CA positions=0
#   Set to 0 when showing side chains from a strand
set cartoon_flat_sheets = 1.0

#   Draw the loops smooth=1 or pass through CA positions=0
#   Set to 0 when showing side chains from a loop
set cartoon_smooth_loops = 0

#   Set the color of the residues
#   to find the names of the colors available
#   click on the rainbow colored square in the
#   upper right corner of the graphics window
#   Here I make some customized colors as mixtures of red,green,blue
set_color maarine=  [0.3, 0.8, 1.0]
set_color graay=[0.8,0.8,0.8]
set_color greeen=[0.0,0.5,0.0]

color gray50, elem C
color greeen, elem ZN
color blue, resid 38:147 and name ca
color yellow, resid 148:397 and name ca
color red, resid 398:514 and name ca

#   Show spheres for chloride ions
show spheres,  elem ZN

#   Show sticks for bonds
show sticks, (resid 173 or resid 175 or resid 177 or resid 242 or resid 253) and not (name n or name c or name o)


set_view (\
     0.091340274,   -0.606698275,    0.789650559,\
    -0.991202235,   -0.131515890,    0.013612081,\
     0.095602803,   -0.783963323,   -0.613382638,\
     0.001799395,    0.001679182, -246.492980957,\
    12.976243019,   41.245639801,   62.928291321,\
   187.538497925,  249.492980957,    0.000000000 )

turn y, 3.5
viewport 1200,1500
ray
png csos3-left.png

Case 2: Ligand-binding sites (Fig. 3; ≥ novice/intermediate)

Active Site Figure

Illustration of the active site of dUTPase from Mycobacterium tuberculosis (PDB ID 1SIX). The orientation of the active site was chosen to feature the geometry of the chemical reaction catalyzed by this enzyme, specifically the in-line nucleophilic attack of water 212 on the alpha-phosphate of dUTP. Fine tuning of the orientation was made to eliminate overlap of side chains and to make all hydrogen bonds (dashed lines) visible. Only side chains directly involved in catalysis are depicted. Carbons are colored according to five conserved motifs of the dUTPase family. Non-conserved residues are given an undistracting gray color and are veiled in fog. Labels were colored to correspond to the side chains they are labeling.

Case 7: Animations (≥ intermediate/advanced)

See the Animations section below.

Animations

M_sV_s

These are just 'ordinary', static figures, as illustrated by the case studied above.