Illustrate: Documentation
Compiling and Running
Compile the fortran code: gfortran illustrate.f -o illustrate
Run the program: illustrate < command_file
Command file is read from unit 5 (standard in), and a bunch of diagnostic stuff is written to unit 6 (standard out)
Command File Format
Command file has command cards (read, center, world, calculate, etc), followed by parameter cards needed for each command
Please issue command cards in this order:
- read — reads coordinates and selection/rendering parameters
- center, translate, xrot, yrot, zrot, scale commands, in any order
- world — defines rendering parameter
- illustrate — defines illustration parameters
- calculate — renders the image and writes ppm file
This program has many idiosyncracies and almost no error checking (beware…postdoc code from the 90s!):
- Selection/rendering cards in the “read” command are read sequentially until one without “ATOM” or “HETATM” is found. Atoms are compared to cards in order, and if a match is found, the atom is assigned those parameters. This process provides a lot of flexibility with very few cards, if you’re clever about the order of cards and the use of wildcards.
- Any number of rotation cards may be added, and they are concatenated when added. This means they are effectively applied last to first, so if you’re progressively refining an orientation, add new rotations to the top of the list.
- Rotations are applied first, then centering, and finally translation. This ensures that the molecule is always centered in the view. Use the translation if you want it offset.
- Origin at upper left, +x down, +y left to right, +z towards viewer, molecules clipped at z=0
About the Outlines
Outlines are created by calculating the local derivative of the z-value using a variety of kernels, then providing a range of values of these derivatives that will be given shades of gray and black. Outlines may be drawn based on the contours and outer shape of the molecule, between subunits, and based on the differences in the residue number in chains.
Sample Command File for PDB entry 2hhb (Hemoglobin)
read #READ command 2hhb.pdb #PDB format coordinate file HETATM-----HOH-- 0,9999, 0.5,0.5,0.5, 0.0 #selection/rendering cards ATOM -H-------- 0,9999, 0.5,0.5,0.5, 0.0 # omits hydrogens ATOM H--------- 0,9999, 0.5,0.5,0.5, 0.0 # omits hydrogens with long atom names ATOM -C-------A 0,9999, 1.0,0.6,0.6, 1.6 # draws carbon atoms in chain A, pink ATOM -S-------A 0,9999, 1.0,0.5,0.5, 1.8 ATOM ---------A 0,9999, 1.0,0.5,0.5, 1.5 # draws the rest of chain A atoms ATOM -C-------C 0,9999, 1.0,0.6,0.6, 1.6 # similarly for chain C ATOM -S-------C 0,9999, 1.0,0.5,0.5, 1.8 ATOM ---------C 0,9999, 1.0,0.5,0.5, 1.5 ATOM -C-------- 0,9999, 1.0,0.8,0.6, 1.6 # draws remaining protein carbons, light orange ATOM -S-------- 0,9999, 1.0,0.7,0.5, 1.8 ATOM ---------- 0,9999, 1.0,0.7,0.5, 1.5 HETATMFE---HEM-- 0,9999, 1.0,0.8,0.0, 1.8 # draws heme iron, yellow HETATM-C---HEM-- 0,9999, 1.0,0.3,0.3, 1.6 HETATM-----HEM-- 0,9999, 1.0,0.1,0.1, 1.5 END #end of READ command center #CENTER command auto #use autocentering trans #TRANSLATION command 0.,0.,0. #x,y,z for translation scale #SCALE command 12.0 #scale value (pixels/A) zrot #ROTATION command 90. #rotation angle (deg) wor #WORLD command (rendering parameters) 1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0 #rgbback, rgbfog, fogparams 1,0.0023,2.0,1.0,0.2 #soft shadow parameters -30,-30 #image size with autosizing illustrate #ILLUSTRATION command 3.0,10.0,4,0.0,5.0 #contour outlines 3.0,10.0 #subunit outlines 3.0,8.0,6000. #residue outlines calculate #CALCULATE command 2hhb.pnm #image file name in ppm
COMMAND CARDS
READ command
PDB filename
Selection/rendering cards
record name (A6) “ATOM “ or “HETATM”, matched with columns 1-6 of PDB file
atom descriptor (A10) matched with columns 13-22 of PDB file, “-” is a wildcard
residue range low, high (integer)
color r,g,b (3 real) 0.0-1.0
radius (real) angstrom, value of 0.0 will omit the atom
CENTER command
centering type (a3)
“aut” (auto) will autocenter with no clipping
“cen” (center) will center on max/min coordinates in xyz
TRANSLATE command
translation vector x,y,z (3 real) translation in Angstroms
XROT, YROT, ZROT commands
rotation angle (real) rotation angle in degrees
SCALE command
scale value (real) pixels/Angstrom
WORLD command
Background and fog parameters
rback r,g,b (3 real) color of background (0.0-1.0)
rfog r,g,b (3 real) color of fog (0.0-1.0)
pfogh, pfogl (2 real) fractional transparency of fog at front and back of molecule
(0.0-1.0, 1.0=no fog)
Soft shadow parameters
icone (integer) 0=no shadows, 1=shadows
pcone (real) fractional shadowing around each atom
larger=darker (0.0-1.0, typically 0.0023)
coneangle (real) angle of shadowing around each atom
larger=tighter region (0.0-1.0, typically 2.0)
rcone (real) shadowing only applied if z-difference greater than this value
(Angstroms, typically 1.0)
pshadowmax (real) maximal shadowing amount
smaller=darker (0.0-1.0, typically 0.7)
ILLUSTRATE command
Contour outline parameters
l_low, l_high (2 real) thresholds for gray to black
typically values from about 3.0-20.0, best values for typical atomic illustrations: 3.0, 10.0
ikernel (integer) kernel for derivative calculation (1,2,3,4 smoothest=4)
l_diff_min, l_diff_max (2 integer) range of z-difference used for derivative (Angstroms)
0.0,1.0 gives outlines around every atom
0.0,1000.0 gives only outline around molecule
0.0,5.0 is typical
Subunit outline parameters
l_low, l_high (2 real) thresholds for gray to black (typically ~ 3.0-20.0)
Residue outline parameters
l_low, l_high (2 real) thresholds for gray to black (typically ~ 3.0-20.0)
resdiff (real) difference in residue numbers to draw outlines
CALCULATE command
Filename for PPM format file