{"id":223,"date":"2019-03-08T00:08:47","date_gmt":"2019-03-08T00:08:47","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/illustrate\/?page_id=223"},"modified":"2019-04-16T03:45:17","modified_gmt":"2019-04-16T03:45:17","slug":"documentation","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/illustrate\/documentation\/","title":{"rendered":"Documentation"},"content":{"rendered":"

Illustrate: Documentation<\/h3><\/h1><\/div>

Compiling and Running<\/h3>\n

Compile the fortran code:<\/em> gfortran illustrate.f -o illustrate<\/span><\/p>\n

Run the program:<\/em> illustrate < command_file<\/span><\/p>\n

Command file is read from unit 5 (standard in), and a bunch of diagnostic stuff is written to unit 6 (standard out)<\/span><\/p>\n

Command File Format<\/h3>\n

Command file has command cards (read, center, world, calculate, etc), followed by parameter cards needed for each command<\/span><\/p>\n

Please issue command cards in this order: <\/span><\/p>\n

    \n
  • \u00a0\u00a0\u00a0 <\/span>read — reads coordinates and selection\/rendering parameters<\/span><\/li>\n
  • \u00a0\u00a0\u00a0 <\/span>center, translate, xrot, yrot, zrot, scale commands, in any order<\/span><\/li>\n
  • \u00a0\u00a0\u00a0 <\/span>world — defines rendering parameter<\/span><\/li>\n
  • \u00a0\u00a0\u00a0 <\/span>illustrate — defines illustration parameters<\/span><\/li>\n
  • \u00a0\u00a0\u00a0 <\/span>calculate — renders the image and writes ppm file<\/span><\/li>\n<\/ul>\n

    This program has many idiosyncracies and almost no error checking (beware…postdoc code from the 90s!):<\/span><\/em><\/p>\n

      \n
    • \u00a0Selection\/rendering cards in the “read” command are read sequentially until one without \u201cATOM\u201d or \u201cHETATM\u201d 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.<\/li>\n
    • 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.<\/span><\/li>\n
    • 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.<\/span><\/li>\n
    • Origin at upper left, +x down, +y left to right, +z towards viewer, molecules clipped at z=0<\/span><\/li>\n<\/ul>\n

      About the Outlines<\/strong><\/p>\n

      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.\u00a0<\/span>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.<\/span><\/p>\n

      Sample Command File for PDB entry 2hhb (Hemoglobin)<\/h3>\n
      read \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0 <\/span>#READ command<\/span>\r\n2hhb.pdb \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0    <\/span>#PDB format coordinate file<\/span>\r\nHETATM-----HOH-- 0,9999, 0.5,0.5,0.5, 0.0 <\/span>\u00a0\u00a0\u00a0    <\/span>#selection\/rendering cards<\/span>\r\nATOM \u00a0-H-------- 0,9999, 0.5,0.5,0.5, 0.0          # omits hydrogens<\/span>\r\nATOM \u00a0H--------- 0,9999, 0.5,0.5,0.5, 0.0          # omits hydrogens with long atom names<\/span>\r\nATOM \u00a0-C-------A 0,9999, 1.0,0.6,0.6, 1.6          # draws carbon atoms in chain A, pink<\/span>\r\nATOM \u00a0-S-------A 0,9999, 1.0,0.5,0.5, 1.8<\/span>\r\nATOM \u00a0---------A 0,9999, 1.0,0.5,0.5, 1.5          # draws the rest of chain A atoms<\/span>\r\nATOM \u00a0-C-------C 0,9999, 1.0,0.6,0.6, 1.6          # similarly for chain C<\/span>\r\nATOM \u00a0-S-------C 0,9999, 1.0,0.5,0.5, 1.8<\/span>\r\nATOM \u00a0---------C 0,9999, 1.0,0.5,0.5, 1.5<\/span>\r\nATOM \u00a0-C-------- 0,9999, 1.0,0.8,0.6, 1.6          # draws remaining protein carbons, light orange<\/span>\r\nATOM \u00a0-S-------- 0,9999, 1.0,0.7,0.5, 1.8<\/span>\r\nATOM \u00a0---------- 0,9999, 1.0,0.7,0.5, 1.5<\/span>\r\nHETATMFE---HEM-- 0,9999, 1.0,0.8,0.0, 1.8          # draws heme iron, yellow<\/span>\r\nHETATM-C---HEM-- 0,9999, 1.0,0.3,0.3, 1.6<\/span>\r\nHETATM-----HEM-- 0,9999, 1.0,0.1,0.1, 1.5<\/span>\r\nEND \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#end of READ command<\/span>\r\ncenter \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0 <\/span>#CENTER command<\/span>\r\nauto \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#use autocentering<\/span>\r\ntrans \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0 <\/span>#TRANSLATION command<\/span>\r\n0.,0.,0. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#x,y,z for translation<\/span>\r\nscale \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0 <\/span>#SCALE command<\/span>\r\n12.0 \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#scale value (pixels\/A)<\/span>\r\nzrot \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0 <\/span>#ROTATION command\r\n90.                                              #rotation angle (deg)\r\n<\/span>wor \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0 <\/span>#WORLD command (rendering parameters)<\/span>\r\n1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0 \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#rgbback, rgbfog, fogparams<\/span>\r\n1,0.0023,2.0,1.0,0.2 \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#soft shadow parameters<\/span>\r\n-30,-30 \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#image size with autosizing<\/span>\r\nillustrate \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0 <\/span>#ILLUSTRATION command<\/span>\r\n3.0,10.0,4,0.0,5.0 \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#contour outlines<\/span>\r\n3.0,10.0 \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#subunit outlines<\/span>\r\n3.0,8.0,6000. \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#residue outlines<\/span>\r\ncalculate \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0 <\/span>#CALCULATE command<\/span>\r\n2hhb.pnm \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span>\u00a0\u00a0\u00a0     <\/span>#image file name in ppm <\/span><\/pre>\n
      COMMAND CARDS<\/h3>\n
      READ command<\/b><\/p>\n
      PDB filename<\/span><\/p>\n
      Selection\/rendering cards<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0<\/span>record name (A6) \u201cATOM \u00a0\u201c or \u201cHETATM\u201d, matched with columns 1-6 of PDB file<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0atom descriptor (A10) matched with columns 13-22 of PDB file, “-” is a wildcard<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0residue range low, high (integer)<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0color r,g,b (3 real) \u00a00.0-1.0<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0radius (real) angstrom, value of 0.0 will omit the atom<\/span><\/p>\n
      CENTER command<\/b><\/p>\n
      centering type (a3)<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u201caut\u201d \u00a0(auto) will autocenter with no clipping<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u201ccen\u201d (center) will center on max\/min coordinates in xyz<\/span><\/p>\n
      TRANSLATE command<\/b><\/p>\n
      translation vector x,y,z (3 real) translation in Angstroms<\/span><\/p>\n
      XROT, YROT, ZROT commands<\/b><\/p>\n
      rotation angle (real) rotation angle in degrees<\/span><\/p>\n
      SCALE command<\/b><\/p>\n
      scale value (real) pixels\/Angstrom<\/span><\/p>\n
      WORLD command<\/b><\/p>\n
      Background and fog parameters<\/span><\/p>\n
      \u00a0 \u00a0 rback r,g,b (3 real) color of background (0.0-1.0)<\/span><\/p>\n
      \u00a0 \u00a0 rfog r,g,b (3 real) color of fog (0.0-1.0)<\/span><\/p>\n
      \u00a0 \u00a0 pfogh, pfogl (2 real) fractional transparency of fog at front and back of molecule<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0(0.0-1.0, 1.0=no fog)<\/span><\/p>\n
      Soft shadow parameters<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>icone (integer) 0=no shadows, 1=shadows<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>pcone (real) fractional shadowing around each atom<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0larger=darker (0.0-1.0, typically 0.0023)<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>coneangle (real) angle of shadowing around each atom<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 larger=tighter region (0.0-1.0, typically 2.0)<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>rcone (real) shadowing only applied if z-difference greater than this value<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0(Angstroms, typically 1.0)<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>pshadowmax (real) maximal shadowing amount<\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 smaller=darker (0.0-1.0, typically 0.7)<\/span><\/p>\n
      ILLUSTRATE command<\/b><\/p>\n
      Contour outline parameters<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>l_low, l_high (2 real) thresholds for gray to black <\/span><\/p>\n
      \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0typically values from about 3.0-20.0, best values for typical atomic illustrations: 3.0, 10.0<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>ikernel (integer) kernel for derivative calculation (1,2,3,4 smoothest=4)<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>l_diff_min, l_diff_max (2 integer) range of z-difference used for derivative (Angstroms)<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0<\/span>\u00a0<\/span>0.0,1.0 gives outlines around every atom<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>0.0,1000.0 gives only outline around molecule<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>0.0,5.0 is typical<\/span><\/p>\n
      Subunit outline parameters<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>l_low, l_high (2 real) thresholds for gray to black (typically ~ 3.0-20.0)<\/span><\/p>\n
      Residue outline parameters<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>l_low, l_high (2 real) thresholds for gray to black (typically ~ 3.0-20.0)<\/span><\/p>\n
      \u00a0\u00a0\u00a0 <\/span>\u00a0\u00a0\u00a0 <\/span>resdiff (real) difference in residue numbers to draw outlines<\/span><\/p>\n
      CALCULATE command<\/b><\/p>\n
      Filename for PPM format file<\/span><\/p>\n<\/div>
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