Program : O2D
Version : 070118
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 596,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : display and conversion of 1D and 2D plot files
Package : X-UTIL/RAVE/DEJAVU
Reference(s) for this program:
* 1 * G.J. Kleywegt (1997). Les amis d"O. CCP4/ESF-EACBM Newsletter on Protein Crystallography 34, September 1997, pp. 5-8. [http://xray.bmc.uu.se/usf/factory_8.html]
* 2 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
921110 - CricketGraph option; auto-update command parameters
930202 - minor changes; updated manual
930203 - minor bug fix (text labels)
930215 - bug fix: PostScript output of 2D contour works with
proper scaling now
930223 - command line option -b(atch) supported: if O2D is run
with this option, no on-screen graphics are possible; hence,
this enables you to do file conversion (plot files to PostScript
or CricketGraph format) without the need for using a workstation
930302 - implemented topology option
930317 - removed bug from cursor routine (now you can't use
the mouse buttons etc in windows other than the
currently selected window; this prevents confusion
and core dumps)
930414 - implemented NAIVE option to quickly plot an "O"-style
datablock file as a 1D line graph
930419 - implemented free-format read for XVALUE and YVALUE in
1D plot files
930607 - implemented GRID in 1D plots
931028 - implemented '*' format and MORE keyword in CricketGraph
conversion option
931129 - prepared for ESV and ALPHA versions
931220 - automatic line dashing with MORE and NEXTFN in PostScript
output file
940215 - 3.2 - cleaned up for manual
940415 - 4.0 - added colour & figure legends; fixed 2D bug
941014 - 4.1 - implemented pie charts
941230 -4.1.1- removed old bug in contour plotting when the
origin was not at (0,0)
951013 - 4.2 - implemented 1D and 2D integration in graphics mode
951014 - 4.3 - added LINE and BOX commands to plot files
951020 - 4.4 - added 1D and 2D integration to popup menu
960415 -4.4.1- minor bug fix
970723 - 4.5 - added Vrml conversion command for 2D plot files
981001 -4.5.1- removed '*' from the first line of CricketGraph
output files (should make the format compatible
with many graphing and spreadsheet programs)
981129 -4.5.2- add some comments to output PostScript files (in
case you want to edit them by hand)
981130 -4.5.3- don't hang on silly viewport (XMIN=XMAX or YMIN=YMAX)
19981216 - 4.6 - HIDE and NOHIDE keywords for 1D, scatter, pie, and
histogram plots to white out everything outside the
plot box (PostScript files only); CIRCLE and ELLIPS
keywords for 1D, scatter, pie, and histogram plots
19990206 - 4.6.1 - DASH and NODASH keywords for 1D, scatter, pie, and
histogram plots to force or suppress dashing of lines
19990824 - 5.0 - new RAMP2D command to produced colour-ramped
boxes instead of contour plots
19990826 -5.0.1- implemented little trick to make the colour-ramped
PostScript files smaller (on average, 2 to 6 times)
19990902 - X - O2D is now also distributed with RAVE and DEJAVU
19990922 -5.0.2- implemented LINFIT keyword for 1D line and
scatter plots to calculate and draw the least-squares
line through the data (assuming unit weights)
19991221 - 5.1 - several changes for Linux/g77
20000628 - 5.2 - implemented XYSTAT keyword for 1D plots to calculate
and print some statistics for the X and Y values as
well as their RMSD and correlation coefficient
20001229 -5.2.1- increased array dimensioning for 1D and 2D plots
20010327 - 5.3 - new BOx_plot (1D) command with BOXPAR keyword
20010427 -5.3.1- minor bug fix (alpha version only)
20010725 -5.3.2- new 1D plot type SPike_plot (mass-spec-like)
20010730 -5.3.3- in BOx plots the average of each bin is now shown
as a "+" sign
20010920 -5.3.4- in BOx plots, the correlation and least-squares
fit of the averages (X and Y) of the boxes are
now also listed (but only boxes that contain at least
10 data points are included in the calculation)
20010924 -5.3.5- minor bug fix
20011011 - 5.4 - new 1D plot type CD_plot (grey-scale mapping of
Y-values; see Jones, T.A. and Kleywegt, G.J. (1999).
CASP3 comparative modelling evaluation. Proteins:
Struct. Funct. Genet. Suppl. 3, 30-46)
20011023 - 5.5 - buffer size for 2D plots can now be passed through
the environment variable or command-line argument
GKBUFFER (e.g.: run o2d gkbuffer 1000000); otherwise,
the default is 500000 points
040701 -5.5.1- changed checks of dynamic memory allocation to allow
for pointers with negative values as returned by
some recent Linux versions
041021 -5.5.2- if the second BOXPAR parameter is negative, it is
interpreted as minus the number of bins and the bins
will be chosen such that they all contain (approx.)
the same number of data points
051125 - 5.6 - implemented COunt_1D_to_2D command which counts the
*distribution* of points in a 1D plot file and produces
a 2D plot file
051205 -5.6.1- minor changes; you can now use 411 predefined colours
070118 -5.6.2- fixed CRICketgraph option which was broken (thanks to
Mark Mayer at NIH for pointing me to the problem)
O2D is small utility program which can be used to produce several types of 1D and 2D display. At present the following types of display are supported:
(a) 1D line graphs (e.g., hydrophobicity versus residue number)
(b) 1D scatter graphs (e.g., phi versus phi for all residues)
(c) 1D histograms, pie-charts, and box plots
(d) 2D contour plots (e.g., CA-CA distance plots or map sections)
(e) colour-ramped 2D plots
(f) topology diagrams produced by DEJAVU
In addition, a simple interface to PostScript exists for the plot options: if you provide a second argument, this is taken to be the name for the output PostScript file; if you give only one argument, no PostScript file will be generated.
A direct connection to "O" does not exist; you are advised to run O2D from a separate window on your workstation. The interactive graphics are only available in the Silicon Graphics version of the program; versions for other machines can be used to do only conversion of plot files to PostScript.
Input plot files can be obtained in several ways:
(1) by editing
(2) from other programs (e.g., MOLEMAN, DATAMAN, OOPS, ODBMAN,
MAPMAN, ODBM, XPLO2D, RMSPDB, LSQMAN, QDB)
(3) raw O datablock files
(4) from scripts (for an example, see OMAC/rfree.csh)
The files (except O datablock files) are simple keyworded
ASCII files, a description is included in this document.
It should be easy to write O2D plot files from your own programs
as well. The plot files created by other programs are
usually very basic; you can easily add "embellishments"
with an editor (change the viewport, add labels, overlay
various plots, change the colours, etc.).
O2D is an interactive, command-driven program. You may create up to eight display windows (this number is merely a parameter, so should you need more, I can easily change it). You may scrutinise/analyse the plots with the mouse. There are three popup menus (toggled through F-keys) for additional manipulation and analysis of the displays. Note that these interactive facilities are available exclusively in the SGI version of the program.
Once you are satisfied with your plots, you may create a tab-delimited ASCII file that can be read by CricketGraph on a Macintosh (note that this only works for 1D plot files and that the keywords 'MORE' and 'NEXTFN' are not supported !). Use this to produce your publication-quality graphs.
If you give the command line argument -b (or -batch), you won't get any on-screen graphics. This allows you to do file conversion (plot file to PostScript, for example) from an ordinary terminal window.
If you start the program, the following output will appear on your screen:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D ***Version - 951013/4.2 (C) 1993-5 Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Fri Oct 13 23:14:03 1995 User - gerard Mode - interactive Host - rigel ProcID - 6938 Tty - /dev/ttyq3
*** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D ***
Reference(s) for this program:
* 1 * G.J. Kleywegt, Uppsala University, Uppsala, Sweden, Unpublished program.
*** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D ***
*** Welcome to the all new XTXgraf grafix routines *** *** By G J Kleywegt & J v/d Zwan - (c) 1991-92 *** *** Current version : 940307/1.2.4 ***
Max nr of graphics windows : ( 8) Max nr of viewport columns : ( 1) Max nr of viewport rows : ( 1) Max number of window objects : ( 10) Max number of viewport objects : ( 10) Total number of graphics objects : ( 168) Max number of popup menus : ( 4)
... GRAPHICS ... Max number of graphics windows : ( 8) Max number of viewport columns : ( 1) Max number of viewport rows : ( 1) Max number of window objects : ( 10) Max number of viewport objects : ( 10) Total number of graphics objects : ( 168) Max number of popup menus : ( 4)
Valid options are: ? ! open_window Dim Name Bkgr_colr Draw_colr select_window [Nr] clear_window cursor_mode Dx Dy naive_1D_plot O_datablock_file [PostScript_file] 1D_line_plot Plot_file [PostScript_file] scatter_plot Plot_file [PostScript_file] histogram Plot_file [PostScript_file] pie_chart Plot_file [PostScript_file] 2D_contour Plot_file [PostScript_file] topology Plot_file [PostScript_file] focus Data_nr integrate Xlo Xhi [Ylo Yhi] close_window cricketgraph Plot_file CricketGraph_file quit
Option ? (open_window) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you run a non-SGI version of O2D, or if you invoke the SGI version with the command-line argument "-b" or "-batch", you get a subset of these commands:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Valid options are: ? ! naive_1D_plot O_datablock_file PostScript_file 1D_line_plot Plot_file PostScript_file scatter_plot Plot_file PostScript_file histogram Plot_file PostScript_file 2D_contour Plot_file PostScript_file cricketgraph Plot_file CricketGraph_file quitOption ? (cricketgraph) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The prompt asks you to supply the name of any of the valid options; the value in parentheses is the default command that will be executed if you just hit the return key. You don't have to type the complete command name; a unique substring suffices. The commands are not case-sensitive; the parameters, however, are !
If a command has parameters, you may provide any number of them on the command line. O2D will prompt you for the values of any parameters which you didn't supply. In these cases, the default value(s) will be shown in parentheses. Hit the Return key to accept a default.
The "no-op" command, i.e. nothing happens (useful if you run O2D from a script and want to insert comments)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window) ! comment Option ? (open_window) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Open a new graphics window. This command has the following parameters:
"Dim" - the "graphics dimension" of the window, being 1 if you
want to use it for 1D plots and 2 otherwise
"Name" - the name of the window (in fact, the number of the
window will be attached to the start of this string)
"Bkgr_colr" - the colour of the background of this window. At present,
SGI colour indices are used (i.e., 0 = black, 7 = white)
"Draw_colr" - the colour for the plot frames and the labels along the
axes
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window) op Dimension [1,2] ? ( 1) Name ? (No_name) 1d_plots Background colour ? ( 0) Drawing colour ? ( 1) 7 Labels ON Opened window : ( 1) Name : (1:1d_plots) Graphics dim : ( 1) Background colour : ( 0) Drawing colour : ( 7) Option ? (open_window 1 1d_plots 0) op 2 2d_plots 0 2 Labels ON Opened window : ( 2) Name : (2:2d_plots) Graphics dim : ( 2) Background colour : ( 0) Drawing colour : ( 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Select window number "Nr". This means that the next operation will take place in this particular window (e.g., a clear, close or plot operation). If you don't supply a value for "Nr", the number of the currently selected window will be shown.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window 2 2d_plots 0) sel 1 Selected window : ( 1) Option ? (select_window 1) sel Selected window : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This erases all graphics objects from the currently selected window, so you can "recycle" it and generate a new plot in it.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (select_window) c ERROR - Invalid or ambiguous option : (c) Option ? (?) cl ERROR - Invalid or ambiguous option : (cl) Option ? (?) cle Labels ON ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Close the currently selected window. If there are any open windows left, the program will select one of them (and tell you which one).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (clear_window) sel 2 Selected window : ( 2) Option ? (select_window 2) clo Active window now : ( 1) Closed window : ( 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Stop working with O2D.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window) quit*** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D ***
Version - 941230/4.1.1 Started - Wed Oct 11 03:01:43 1995 Stopped - Wed Oct 11 03:04:59 1995
CPU-time taken : User - 0.1 Sys - 0.2 Total - 0.3
*** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D ***
>>> This program (C) 1993-95, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** O2D *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Produces a 1D line graph in the currently selected window (must be 1D !), by processing the instruction file "Plot_file" (see below).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (close_window) 1d 1rbp_mc_b.plt 1rbp_mc.ps Initialising ... Reading ... Plotting ... New VPT object : (1D_plot) => XPS_GRAF - GJK (931220/1.2) Opened PostScript file : (1rbp_mc.ps) Date : (Wed Feb 16 01:36:48 1994) User : (gerard) Program : (O2D) Number of data points : ( 329) Lowest X-value : ( 1.000E+00) Highest X-value : ( 3.290E+02) Lowest Y-value : ( 0.000E+00) Highest Y-value : ( 7.264E+01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Produces a 1D box plot in the currently selected window (must be 1D !),
by processing the instruction file "Plot_file" (see below). The
behaviour can be affected with the BOXPAR keyword in the plot
file which has the following parameters:
- BOXLOW = lower limit for X-coordinates
- BOXBIN = bin size (all points in a bin are lumped)
- BOXMAX = upper limit for X-coordinates
A box plot shows for each bin the 10th, 25th, 50th (median), 75th and 90th percentile of the (Y-values of the) points in the bin. All the extreme points (the 10% above the 90th percentile and the 10% below the 10th percentile) are shown individually (using symbols as for a scatter plot). Statistics for each bin are printed. Note: for bins that contain 10 or fewer points the percentiles are not calculated and only the individual points are shown. For an example, see Figures 2 and 3 in U Dengler, AS Siddiqui & GJ Barton, Proteins 42, 332-344 (2001).
As of version 5.5.2, if the BOXBIN parameter is negative then it is interpreted as minus the number of bins and the bins will be chosen such that they all contain (approx.) the same number of data points.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Option ? (open_window 1 11 0 1) box box.plt box.ps
Initialising ...
Reading ...
> (Created by ODBMAN V. 001206/1.9.5 at Mon Dec 11 17:05:17 2000 for
gerard)
> (Scatter plot of datablock (X) YEAR)
> (And datablock (Y) RFREE)
> (X ave,sdv,min,max = 1.9978E+03 1.3548E+00 1.9930E+03
2.0000E+03)
> (Y ave,sdv,min,max = 2.5463E-01 3.8939E-02 6.7600E-02
4.6500E-01)
> (X-Y corr. coeff., rmsd = -0.057 1.9975E+03)
Free format read
Free format read
Plotting ...
Linear fit: slope -1.6459E-03 ... intercept 3.5428E+00
New VPT object : (box_plot)
=> XPS_GRAF - GJK (19981216/3.1.2)
Opened PostScript file : (box.ps)
Date : (Tue Mar 27 22:04:40 2001)
User : (gerard)
Program : (O2D)
X-min X-max Nr
1.9925E+03 1.9935E+03 6
Average St.dev. Minimum Maximum Ave-2*Sdv Ave+2*Sdv
2.632E-01 4.832E-02 2.250E-01 3.640E-01 1.665E-01 3.598E-01
[...]
X-min X-max Nr Median 25th % 75th % 10th % 90th %
1.9995E+03 2.0005E+03 323 2.530E-01 2.300E-01 2.700E-01 2.140E-01 2.913E-01
Average St.dev. Minimum Maximum Ave-2*Sdv Ave+2*Sdv
2.518E-01 3.308E-02 9.400E-02 3.760E-01 1.856E-01 3.180E-01
Nr of extras : ( 0)
Number of data points : ( 5112)
Lowest X-value : ( 1.992E+03)
Highest X-value : ( 2.001E+03)
Lowest Y-value : ( 0.000E+00)
Highest Y-value : ( 5.000E-01)
CPU total/user/sys : 1.6 1.5 0.1
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Produces a 1D scatter graph in the currently selected window (must be 1D !), by processing the instruction file "Plot_file" (see below).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (clear_window) sel 1 Selected window : ( 1) Option ? (select_window 1) clea Labels ON Option ? (clear_window) sc p2a_flip_p2a_rsc.plt p2a_flip_p2a_rsc.ps Initialising ... Reading ... Plotting ... New VPT object : (scatter_plot) => XPS_GRAF - GJK (931220/1.2) Opened PostScript file : (p2a_flip_p2a_rsc.ps) Date : (Wed Feb 16 01:40:43 1994) User : (gerard) Program : (O2D) Number of data points : ( 131) Lowest X-value : ( -1.852E-01) Highest X-value : ( 3.890E+00) Lowest Y-value : ( -2.622E-01) Highest Y-value : ( 5.506E+00) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Produces a normal 1D line plot in the currently selected window (must be 1D !), by processing the instruction file "Plot_file" (see below). The PostScript file, however, will contain a "CD plot" in which the Y-values are been used to calculate a grey-scale value for each X (low = white; high = black). For examples, see Jones, T.A. and Kleywegt, G.J. (1999). CASP3 comparative modelling evaluation. Proteins: Struct. Funct. Genet. Suppl. 3, 30-46).
The keyword CDVERT can be used to supply a number between 0.01 and 1.0 (default is 0.1) that defines the fraction of the Y-axis of the plot that should be used.
For an example of a CD plot, look here.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window 1 1 0 1) cd m1_multi_rms_dist.plt q.ps Plot type : (CDPLOT) Initialising ... Reading ... > (Created by LSQMAN V. 010906/8.5 at Thu Oct 11 18:38:03 2001 for gerard) > (Plot of Multi-RMS (distances between all unique pairs) as a function of residue nr) > (Atom type used CA) > (Values are for mol M1 = file pdb1ldn.ent) Free format read > (Multi-RMS ave, sdv, min, max 0.36 0.28 0.17 3.27) Free format read Plotting ... New VPT object : (CD_plot) => XPS_GRAF - GJK (19981216/3.1.2) Opened PostScript file : (q.ps) Date : (Thu Oct 11 21:56:42 2001) User : (gerard) Program : (O2D) CDVERT : ( 0.100) CDYMAX : ( 0.359) Nr of extras : ( 0) Number of data points : ( 316) Lowest X-value : ( 1.400E+01) Highest X-value : ( 3.310E+02) Lowest Y-value : ( 0.000E+00) Highest Y-value : ( 3.590E+00) CPU total/user/sys : 1.2 1.1 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Produces a 1D spike plot in the currently selected window (must be 1D !), by processing the instruction file "Plot_file" (see below). This looks a bit like a mass spectrum with every point represented as a line from (x,0) to (x,y).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window 1 1 0 1) spike m1_multi_rms_dist.plt q.ps Plot type : (SPIKE) Initialising ... Reading ... [...] Plotting ... New VPT object : (spike_plot) => XPS_GRAF - GJK (19981216/3.1.2) Opened PostScript file : (q.ps) Date : (Thu Oct 21 19:19:25 2004) User : (gerard) Program : (O2D) Nr of extras : ( 0) Number of data points : ( 316) Lowest X-value : ( 1.400E+01) Highest X-value : ( 3.310E+02) Lowest Y-value : ( 0.000E+00) Highest Y-value : ( 3.590E+00) CPU total/user/sys : 3.3 3.2 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Produces a colour-ramped 2D plot in the currently selected window (must be 2D !), by processing the instruction file "Plot_file" (see below). The colour-ramped plot *only* appears in the PostScript file ! On the display you will see a contour plot as usual. There are several plot file commands specifically for controlling the ramping:
- RAMLIM: sets the limits for the "low" and "high" colours (values
below or above these limits will be ramped to the extreme
colours); default = entire dynamic range
- RAMCOL: RGB values for the "low" and the "high" colours; default
is from blue to red
- RAMODE: LINear, LOGarithmic or ABSolute. If your data has a very
large dynamic range, you may want to apply LOG scaling. If your
data has positive and negative values (e.g., a difference-distance
plot from LSQMAN) and you are only interested in the absolute
values, use ABS.
- RAMTYP: defines the type of ramping. The default is HUE, which
will ramp, e.g., from blue to red via green etc. If you want
to ramp from or to white, use SAT(uration) instead (and make
sure that one of the two RAMCOLs is white). If you want to
ramp from black to white or vice versa, use VAL(ue) (and make
sure that the RAMCOLs are black and whte). If you want to ramp
from one colour to another via white, use WHI(te).
Compare the following plots:
- ordinary contour plot (of leucine chi1/chi2 combinations)
here
- hue-ramped from blue to red (log-scaled)
here
- sat-ramped from white to green (log-scaled)
here
- val-ramped from white to black (log-scaled)
here
- white-ramped from blue to white to red (log-scaled)
here
As for RGB colours, they are triples of numbers, either in the
range [0.0,1.0], or in the range [0,256]. O2D will divide any
RGB values greater than 1.0 by 256, so you can use either
convention. On SGIs, use the "cedit" program to find RGB colour
values. Useful ones are:
- black = 0 0 0
- white = 1 1 1
- grey = X X X (i.e., the same number for R, G and B)
- red = 1 0 0
- green = 0 1 0
- blue = 0 0 1
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Option ? (open_window 2 2 0 1) ramp_2d leu_rotamers.plt log_sat.ps
FREE format read
> (Total nr of residues 28268)
> (Cut-off for local maxima 40)
> (Local maximum 494 @ 177.5 62.5)
> (Local maximum 46 @ -97.5 22.5)
> (Local maximum 775 @ -62.5 177.5)
New VPT object : (ramp_2D)
=> XPS_GRAF - GJK (19981216/3.1.2)
Opened PostScript file : (log_sat.ps)
Date : (Tue Aug 24 22:55:12 1999)
User : (gerard)
Program : (O2D)
Ramp mode : LOGARITHMIC
Ramp type : SATURATION
Limit : ( 0.000E+00)
RGB start : ( 1.000 1.000 1.000)
Limit : ( 2.700E+00)
RGB end : ( 0.000 1.000 0.000)
SAT start : ( 0.000)
SAT end : ( 1.000)
Nr of extras : ( 0)
Number of data points : ( 5329)
Lowest X-value : ( 0.000E+00)
Highest X-value : ( 3.600E+02)
Lowest Y-value : ( 0.000E+00)
Highest Y-value : ( 3.600E+02)
Number of levels : ( 10)
Level intensities : ( 5.000E+00 1.000E+01 2.500E+01 4.000E+01
5.500E+01 7.500E+01 1.000E+02 1.250E+02 2.500E+02 5.000E+02)
Level colour indices : ( 1 1 1 2
2 3 3 4 5 6)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Produces a 2D contour plot in the currently selected window (must be 2D !), by processing the instruction file "Plot_file" (see below).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window 2 2d_plots 0) 2d ca_ca_1rbp.plt ca_ca_1rbp.ps Formatted read New VPT object : (2D_plot) => XPS_GRAF - GJK (931220/1.2) Opened PostScript file : (ca_ca_1rbp.ps) Date : (Wed Feb 16 01:41:27 1994) User : (gerard) Program : (O2D) Number of data points : ( 30276) Lowest X-value : ( 1.000E+00) Highest X-value : ( 1.740E+02) Lowest Y-value : ( 1.000E+00) Highest Y-value : ( 1.740E+02) Number of levels : ( 3) Level intensities : ( 3.000E+00 6.000E+00 1.100E+01) Level colour indices : ( 1 2 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Plot 1D data as a histogram.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (2d_plot ca_ca_1rbp.plt ca_ca_1rbp.ps) sel 1 Selected window : ( 1) Option ? (select_window 1) histo p2a_rsc.plt Initialising ... Reading ... Plotting ... New VPT object : (histogram) Number of data points : ( 130) Lowest X-value : ( 0.000E+00) Highest X-value : ( 1.320E+02) Lowest Y-value : ( 0.000E+00) Highest Y-value : ( 4.000E+00) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Plot 1D histogram data as a pie-chart.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window 1 1 0 1) pie pie.plt pie.ps Initialising ... Reading ... Format : ((1p,5e15.7)) Format : ((5f15.0)) Plotting ... New VPT object : (pie) => XPS_GRAF - GJK (2.0 @ 940415) Opened PostScript file : (pie.ps) Date : (Fri Oct 14 01:55:06 1994) User : (gerard) Program : (O2D) A 13.00000 between 0.2000000 and 0.4000000 B 33.00000 between 0.4000000 and 0.6000000 C 60.00000 between 0.6000000 and 0.8000000 D 68.00000 between 0.8000000 and 1.000000 E 57.00000 between 1.000000 and 1.200000 F 44.00000 between 1.200000 and 1.400000 G 19.00000 between 1.400000 and 1.600000 H 23.00000 between 1.600000 and 1.800000 I 6.000000 between 1.800000 and 2.000000 J 4.000000 between 2.000000 and 2.500000 Number of data points : ( 10) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Takes an O datablock and produces a simple 1D line graph (if you want more fancy plots, generate a plot file, either with an editor, or with ODBM or ODBMAN).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (histogram p2a_rsc.plt p2a_rsc.ps) sel 1 Selected window : ( 1) Option ? (select_window 1) cle Labels ON Option ? (clear_window) nai p2a_flip.o p2a_flip.ps Initialising ... Reading ... Label : (P2A_RESIDUE_PEPFLIP) Type : (R) Format : ((10(x,f7.5))) Number : ( 131) Plotting ... New VPT object : (1D_plot) => XPS_GRAF - GJK (931220/1.2) Opened PostScript file : (p2a_flip.ps) Date : (Wed Feb 16 01:43:42 1994) User : (gerard) Program : (O2D) Number of data points : ( 131) Lowest X-value : ( 1.000E+00) Highest X-value : ( 1.310E+02) Lowest Y-value : ( 0.000E+00) Highest Y-value : ( 3.705E+00) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
DEJAVU can produce (too simple) topology files which can be drawn with this command. The results are not impressive (methinks).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (naive p2a_flip.o p2a_flip.ps) op 2 topo 0 6 Labels ON Opened window : ( 3) Name : (3:topo) Graphics dim : ( 2) Background colour : ( 0) Drawing colour : ( 6) Option ? (open_window 2 topo 0) topo cbh6a.topo cbh6a_topo.ps New VPT object : (topology) => XPS_GRAF - GJK (931220/1.2) Opened PostScript file : (cbh6a_topo.ps) Date : (Wed Feb 16 01:44:49 1994) User : (gerard) Program : (O2D) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Converts a 2D plot file into a VRML file. For what it's worth.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (cricketgraph) vr test.pl2 test.wrl s > (Created by MAPMAN V. 970501/5.1 at Wed Jul 23 18:42:49 1997 for user gerard) > (Contour plot of X-Z plane nr 70) > (Map M2) > (File p2.mask) > (Comment Read from p2.mask) > (Cell 91.80 99.50 56.50 90.00 90.00 90.00) > (Grid 100 110 64) Formatted read Opened VRML file Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This commands reads a 1D plot file, divides the axes in a number of bins (you can determine those yourself if you like with the XCOUNT and YCOUNT keywords in the plot file), and counts the number of points in each 2D bin. The 2D distribution is subsequently written to a 2D O2D plot file which you can then plot with the 2D or RAmp commands (optionally, after editing the 2D plot file to change the default colours, level, colour-ramping parameters, labels, etc.).
The XCOUNT and YCOUNT keywords have three arguments, the minimum value, bin size, and maximum value to take into account along X or Y, respectively. Note that the actual data may extend outside these limits - points outside them will simply not be counted.
In the 2D plot file, by default there will be 10 plot levels corresponding to 9%, 18%, 27%, ..., 90% of the maximum count found in anyone bin. The colours of these levels are also predefined. The default colour-ramp parameters will produce a HUE-ramped plot from red to blue. Of course, you can change all these things by simply editing the 2D plot file before plotting it.
This command is useful when you have a large dataset for which a normal scatter plot becomes too cluttered. An alternative is a BOx_plot, but these don't show how densely the various bins are populated (and the binning is only done for the X axis).
Suppose you want to plot the R-value versus resolution for several thousand PDB entries. Compare the following plots:
- simple 1D scatter plot (very cluttered)
here
- 1D box plot (better but no idea how densely populated the bins are)
here
- 2D contour plot (after conversion with the COunt_1D_to_2D command)
here
- colour-ramped 2D plot (after conversion with the COunt_1D_to_2D command)
here
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Option ? (open_window 2 2 0 1) cou mapr_vs_resolution.plt mapr_vs_resolution.pl2
Reading 1D plot file ...
Keyword ignored : (BOXPAR)
Keyword ignored : (XYVIEW)
Keyword ignored : (MRKSIZ)
> (Created by ODBMAN V. 040618/2.2.3 at Tue Nov 22 15:00:58 2005 for A.
Nonymous)
> (Scatter plot of datablock (X) RESOLUTION)
> (And datablock (Y) MAPR)
> (X ave,sdv,min,max = 2.0675E+00 4.6045E-01 8.0000E-01
4.0000E+00)
> (Y ave,sdv,min,max = 2.1050E-01 3.5745E-02 7.1000E-02
3.5900E-01)
> (X-Y corr. coeff., rmsd = 0.584 1.9085E+00)
Keyword ignored : (LINFIT)
Keyword ignored : (COLOUR)
Nr of data points : ( 8653)
Binning and counting ...
Xmin, Xmax, Xbin, Nxbin = 6.5000E-01 4.0500E+00 1.0000E-01 35
Ymin, Ymax, Ybin, Nybin = 0.0000E+00 3.7000E-01 1.0000E-02 38
Nr of points binned : ( 8653)
Max count in any bin : ( 147)
Writing 2D plot file ...
2D plot file written
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The 2D plot file created in this fashion may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMARK Created by O2D V. 051125/5.6 at Fri Nov 25 23:38:11 2005 for gerard [...] REMARK X-Y corr. coeff., rmsd = 0.584 1.9085E+00 NLEVEL 10 LEVELS 13 26 40 53 66 79 93 106 119 132 COLOUR 1 2 3 3 4 4 5 5 6 6 RAMCOL 1 0 0 0 0 1 RAMTYP HUE XLABEL Value of RESOLUTION YLABEL Value of MAPR XPOINT 35 YPOINT 38 XLIMIT 6.5000E-01 4.0500E+00 YLIMIT 0.0000E+00 3.7000E-01 ZVALUE * 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [...] 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 4 9 18 50 55 92 112 147 139 74 78 65 28 50 19 16 13 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Converts a plot file into a CricketGraph file. Note: Swedish versions of CG and/or the Mac operating system use decimal comma's instead of decimal points; these can therefore not read the CG files produced by O2D
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (select_window 3) cr p2a_flip.plt p2a_flip.cg Nr of data points : ( 131) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix > cat p2a_flip.cg * Residue Pep_flip 1.00000 0.00000 2.00000 0.00000 3.00000 1.43300 4.00000 0.40947 5.00000 2.53970 6.00000 1.55600 7.00000 0.53990 8.00000 0.95495 9.00000 1.62520 10.00000 3.70480 11.00000 3.49990 12.00000 2.81690 ... 128.00000 0.40391 129.00000 0.93459 130.00000 0.00000 131.00000 0.00000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This option can only be used with 1D graphs. You provide a data point index (e.g., a residue number) and the program will zoom in on that particular data point: the point will be displayed at the centre of the window, with margins of 1 % of the display width to all four sides.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (foc) foc Data point number ? ( 432) 55 Option ? (foc) foc 123 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Integrate part of a 1D curve, or part of a 2D contour map.
1D: simply provide the lower and upper X coordinates of the points
between which you want to integrate the curve. Use the cursor_mode
to find suitable integration limits, if necessary.
The following example shows how CHI1 angles of Valine residues are
distributed in high-resolution structures (>70% has CHI=180):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (open_window) op 1 1 0 1 ... Option ? (open_window 1 1 0 1) 1d val_chi1.plt ... Option ? (1d_plot val_chi1.plt) cu 10 10 Horizontal arrow step : ( 10.000) Vertical arrow step : ( 10.000) Column,row,x,y : 1 1 48.235 105.857 48.235 105.857 Column,row,x,y : 1 1 86.667 127.571 86.667 127.571 Column,row,x,y : 1 1 140.784 168.286 140.784 168.286 Column,row,x,y : 1 1 201.569 181.857 201.569 181.857 Column,row,x,y : 1 1 271.765 190.000 271.765 190.000 Column,row,x,y : 1 1 320.000 192.714 320.000 192.714 Option ? (cursor_mode 10 10) int 48 87 Integrated 40 points between 4.8000E+01 and 8.7000E+01 Actual integration limits found 4.8000E+01 and 8.7000E+01 Integral = 1.6160E+03 Total curve integral = 2.4725E+04 Average value = 4.0400E+01 Total curve average = 6.8490E+01 Fraction of total = 0.0654 Centre of gravity = 6.6475E+01 Option ? (integrate 48 87) in 202 140 Integrated 63 points between 1.4000E+02 and 2.0200E+02 Actual integration limits found 1.4000E+02 and 2.0200E+02 Integral = 1.7410E+04 Total curve integral = 2.4725E+04 Average value = 2.7635E+02 Total curve average = 6.8490E+01 Fraction of total = 0.7041 Centre of gravity = 1.7462E+02 Option ? (integrate 202 140) in 271 320 Integrated 50 points between 2.7100E+02 and 3.2000E+02 Actual integration limits found 2.7100E+02 and 3.2000E+02 Integral = 4.2760E+03 Total curve integral = 2.4725E+04 Average value = 8.5520E+01 Total curve average = 6.8490E+01 Fraction of total = 0.1729 Centre of gravity = 2.9726E+02 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2D: provide the X and Y boundaries for integration. Note that this can
*only* be used for the last 2D contour plot that you made, since the
data are not stored for earlier plots !!!
The following example shows how CHI1/CHI2 rotamers of Leucine residues are
distributed in high-resolution structures (55 % + 26 % for the two
major rotamers):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (integrate 271 320) op 2 2 0 1 ... Option ? (open_window 2 2 0 1) 2d leu_rotamers.plt ... Option ? (2d_plot leu_rotamers.plt) cu 10 10 Horizontal arrow step : ( 10.000) Vertical arrow step : ( 10.000) Column,row,x,y : 1 1 252.382 210.517 252.382 210.517 Column,row,x,y : 1 1 327.223 134.483 327.223 134.483 Column,row,x,y : 1 1 148.042 97.241 148.042 97.241 Column,row,x,y : 1 1 214.689 29.483 214.689 29.483 Column,row,x,y : 1 1 223.429 67.241 223.429 67.241 Column,row,x,y : 1 1 289.530 3.621 289.530 3.621 Option ? (cursor_mode 10 10) in 250 330 210 130 Integrated 289 points X range 2.5000E+02 to 3.3000E+02 ( 2.5000E+02 3.3000E+02) Y range 1.3000E+02 to 2.1000E+02 ( 1.3000E+02 2.1000E+02) Integral = 1.5638E+04 Total curve integral = 2.8268E+04 Average value = 5.4111E+01 Total curve average = 5.3046E+00 Fraction of total = 0.5532 Centre of gravity = 2.9685E+02 1.7768E+02 Option ? (integrate 250 330 210 130) in 145 215 30 100 Integrated 225 points X range 1.4500E+02 to 2.1500E+02 ( 1.4500E+02 2.1500E+02) Y range 3.0000E+01 to 1.0000E+02 ( 3.0000E+01 1.0000E+02) Integral = 7.4380E+03 Total curve integral = 2.8268E+04 Average value = 3.3058E+01 Total curve average = 5.3046E+00 Fraction of total = 0.2631 Centre of gravity = 1.8313E+02 6.7417E+01 Option ? (integrate 145 215 30 100) in 220 290 0 70 Integrated 225 points X range 2.2000E+02 to 2.9000E+02 ( 2.2000E+02 2.9000E+02) Y range 0.0000E+00 to 7.0000E+01 ( 0.0000E+00 7.0000E+01) Integral = 2.1810E+03 Total curve integral = 2.8268E+04 Average value = 9.6933E+00 Total curve average = 5.3046E+00 Fraction of total = 0.0772 Centre of gravity = 2.6225E+02 3.9519E+01 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note: these integration options have also been built into one of the cursor-mode popup menus, so you can integrate interactively.
With this command you enter the cursor analysis mode. You have the following controls:
ESC-key to QUIT cursor mode (or appropriate popup items)
PAN with left mouse button or arrow keys
ZOOM with middle mouse button
F-KEYS to toggle popup menus
POPUPS are activated by the right mouse button
^ in a popup means that cursor position is used
^^ in a popup means that you have to select an area
If you pan with the arrow keys, you move in horizontal steps "Dx" and
vertical steps "Dy". If you pan with the left mouse button, the distance
that you cover is proportional to the time between pressing and releasing
the mouse button. The same, mutatis mutandis, holds when you're zooming
with the mouse; moving left zooms in horizontally, moving down zooms in
vertically (hence, move towards the top righthand corner if you want to
zoom out in both directions, etc.).
If you have to select an area (e.g., when you use the popup option "zoom
area ^^"), move the cursor to one of the corners, click the right mouse
button and keep it down; then move to the other corner (the first corner
will be highlighted while you do this) and release the mouse button.
NOTE: you can only analyse one window at a time, namely the currently selected one !!! So even though you may be pressing the arrow keys in another window, the selected window's plot will actually move ! If you want to switch to analysing another plot, you have to select that window (use the "next window" option of the Manipulate popup, vide infra).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (focus 48) cu 5 .1 Horizontal arrow step : ( 5.000) Vertical arrow step : ( 0.100)ESC-key to QUIT cursor mode PAN with left mouse button or arrow keys ZOOM with middle mouse button F-KEYS to toggle popup menus ^ in popup means cursor position is used ^^ in popup means you have to pick a 2D area
F-key menus : F 1 : Manipulate F 2 : Analyse F 3 : General_menu
Popup menu : (Manipulate) 47.71374 1.300776 Point # 48 (D = 2.9309E-04) X,Y,Label = 4.8000E+01, 1.2902E+00 |Data_pt_48| Popup menu : (Analyse) Data points with Y > 2.491559 Point # 5 X,Y,Label = 5.0000E+00, 2.5397E+00 |Data_pt_5| Point # 10 X,Y,Label = 1.0000E+01, 3.7048E+00 |Data_pt_10| Point # 11 X,Y,Label = 1.1000E+01, 3.4999E+00 |Data_pt_11| Point # 12 X,Y,Label = 1.2000E+01, 2.8169E+00 |Data_pt_12| Point # 13 X,Y,Label = 1.3000E+01, 3.4269E+00 |Data_pt_13| Point # 46 X,Y,Label = 4.6000E+01, 2.8258E+00 |Data_pt_46| Point # 97 X,Y,Label = 9.7000E+01, 2.6618E+00 |Data_pt_97| Point # 117 X,Y,Label = 1.1700E+02, 3.2989E+00 |Data_pt_117| Popup menu : (General_menu) Popup menu : (Manipulate) Horizontal line at Y = ( 2.427E+00) Selected window : ( 2) ERROR --- Not a 1D window 79.98586 105.2047 Selected window : ( 3) ERROR --- Not a 1D window Selected window : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
At present, there are three popup menus, one general (handled by the graphics routines, called "General" and activated with the F3 key) and two specific for O2D (called "Manipulate", activated through F1 and "Analyse", activated through F2). They contain the following options:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ________________________________ | GENERAL popup | ACTION: ________________________________ ________________________________ | zoom area ^^ | zoom in on a specific part of your plot ________________________________ | location ^ | print current cursor position ________________________________ | pop text port | pop text window to front | push text port | push text window to back ________________________________ | help | print summary of controls | list menus | list menu names and their F-keys ________________________________ | double horizontal arrow step | multiply "Dx" by 2.0 | halve horizontal arrow step | multiply "Dx" by 0.5 | double vertical arrow step | multiply "Dy" by 2.0 | halve vertical arrow step | multiply "Dy" by 0.5 ________________________________ | integrate curve/area ^^ | integrate part of 1D or 2D plot ________________________________ | QUIT cursor mode | go back to the O2D command loop level ________________________________ ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ________________________________ | MANIPULATE popup | ACTION: ________________________________ ________________________________ | ID data point ^ | print coordinates and label of closest point | location ^ | print current cursor location ________________________________ | reset full viewport | reset original, complete view of the plot | next window | select the next window for analysis ________________________________ | display one label ^ | plot label of closest data point | display all labels | plot all labels ________________________________ | draw horizontal line ^ | draw horizontal line at cursor position | draw vertical line ^ | draw vertical line at cursor position | draw cross lines ^ | draw horizontal and vertical line ________________________________ | quit cursor mode | go back to the O2D command loop level ________________________________ | QUIT O2D | quit working with O2D alltogether ________________________________ ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ________________________________ | ANALYSE popup | ACTION: ________________________________ ________________________________ | List data Y > cursor ^ | list data points above the cursor position | List data Y < cursor ^ | list data points below the cursor position | quit cursor mode | go back to the O2D command loop level ________________________________ | QUIT O2D | quit working with O2D alltogether ________________________________ ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The plot instruction files are simple keyworded ASCII files which may contain
pointers to "O"-datablock files in certain places.
Records in the plot instruction files contain a keyword, one space and (usually)
some data which is read into a string and parsed depending on the value of the
keyword. The format for such lines is: (A6,1X,A), where the string may be up to
80 characters in length. Keywords are not case-sensitive.
For both 1D and 2D files, any line which has an exclamation mark "!" in column one of the keyword, or which has the keyword "REMARK", is treated as a comment line. The end of a file may be signaled by the keyword "END " or by an end-of- file.
Ready-made 1D plot files are generated many USF programs, including MAPMAN, DATAMAN, LSQMAN, MOLEMAN(2), ODBM(AN), OOPS(2), RMSPDB and XPLO2D.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Keyword Format Type Rest of the line
-------------------------------------------------------------------------------
# NPOINT (*) (I) nr of data points
COLOUR (*) (I) colour index for drawing the graph/points
XYVIEW (*) (4R) define the area to be displayed on the screen by
providing XMIN, XMAX, YMIN and YMAX; use this keyword
to compare different files on the same scale
MRKTYP (*) (I) marker type; this is for scatter graphs only; the
following options are supported: 1 = plus, 2 = cross,
3 = Z, 4 = diamond, 5 = triangle (pointing up),
6 = triangle (down), 7 = triangle (left), 8 = triangle
(right), all other values = box
MRKSIZ (*) (2R) horizontal and vertical sizes of the markers
# XLABEL (A) (A) label for marking the horizontal axis
# YLABEL (A) (A) label for marking the vertical axis
# XLIMIT (*) (2R) lower value for X and the increment (requires NPOINT)
# YLIMIT (*) (2R) lower value for Y and the increment (requires NPOINT)
# XVALUE (A) (A) format for reading explicit X values from the following
records (requires NPOINT); * = free format
# YVALUE (A) (A) format for reading explicit Y values from the following
records (requires NPOINT); * = free format
LABELS (A) (A) format for reading explicit data point labels from the
following records (requires NPOINT)
# XFROMO (A) (A) filename of an "O" datablock from which the X values are
to be read
# YFROMO (A) (A) filename of an "O" datablock from which the Y values are
to be read
LFROMO (A) (A) filename of an "O" datablock from which the labels are
to be read
# VALUES (A) (A) format for reading explicit X and Y value pairs from the
following records (requires NPOINT); * = free format
# VALABS (A) (A) format for reading explicit X/Y/label triples from the
following records (requires NPOINT)
NEXTFN (A) (A) more data will be read from the next file whose name
should be on the rest of this line
MORE --- --- plot the current points and then continue reading from
the current file (a convenient way of plotting multiple
curves in one graph)
TEXT (*) (3R,A) draw a text label; the three arguments are: X, Y position
for the text label, the size in points (only used for the
PostScript output file) and the text itself (enclose in
SINGLE QUOTES !!!)
GRID (*) (6R) draw a grid; the six arguments are: x-start, x-end,
x-spacing, y-start, y-end, y-spacing
LINE (*) (4R) X1,Y1, X2,Y2; draws line from (X1,Y1) to (X2,Y2)
BOX (*) (4R) XLO,XHI, YLO,YHI; draws a box
CIRCLE (*) (3R) Xcentre,Ycentre,Radius; draws a circle
ELLIPS (*) (4R) Xcentre,Ycentre,Xradius,Yradius; draws an ellipse
HIDE --- --- in PostScript output file, white out area outside plot box
NOHIDE --- --- in PostScript output file, do NOT white out area outside
plot box
DASH --- --- in PostScript output file, force dashing level to be incremented
NODASH --- --- in PostScript output file, re-set solid line type
LINFIT --- --- will calculate the least-squares fit through the data;
for line and scatter plots this line will also be drawn
XYSTAT --- --- will calculate and print stats for X, Y and correlation coeff.
BOXPAR (*) (3R) values of BOXLOW, BOXBIN and BOXMAX for box plots
CDVERT (*) (R) fraction of vertical axis that is to be used in CD plots
XCOUNT (*) (3R) values for XLOW, XBIN and XMAX for count_1d_to_2d command
YCOUNT (*) (3R) values for YLOW, YBIN and YMAX for count_1d_to_2d command
# END --- --- stop reading; ignore the rest of the input file
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that only a few of the available keywords are actually used in any one file. For example, one may obtain X-values either by enumeration (option XLIMIT), or explicitly from any of the options XVALUE, XFROMO, VALUES or VALABS. By default, all X and Y values are 1, 2, 3 etc., so if that's what you want, you don't even have to use any of these options. In addition, the labels are set by default to "Data_pt_1" etc. for consecutive points.
The keywords marked with an "#" in front of them are also supported by the CricketGraph conversion routine (the others are simply ignored).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Example 1D plot file ! NPOINT 300 ! X runs from 1 to 301 XLIMIT 1 1 XLABEL sequence YLABEL attribute ! draw plot in yellow COLOUR 3 MRKSIZ 5 50 ! use triangles in scatter plots MRKTYP 5 ! explicit Y values YVALUE (15F5.0) 1485 884 648 581 2563 3758 2040 860 -64-1552 -425 1265 403 -203 405 775 532 -756-1184 243 665 1654 128 160 538 2289 3019 1550 1019 -131 -2154 -385 2119 943 71 838 744 548 814 1177 1554 1111 907 780 1583 ... -1781 -120 299 -331 822 2014 1036 109 -352-1286 -828 -280-2052-2288 95 -392-2683-1815 232 -17 -415 451 1929 1851 985 1591 2220 1881 2722 3236 1699 1334 1185-1962-3371 -619 -239-3278-3806 1604 1668 1349 2122 2746 1712 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Example 1D plot file ! ! use residue numbers for X XFROMO am_residue_irc ! plot PepFlip values as function of residue nr YFROMO am_residue_pepflip ! labels axes XLABEL Sequence YLABEL PepFlip ! draw plots in green COLOUR 2 MRKSIZ 0.75 0.02 ! use crosses in scatter graphs MRKTYP 2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- NPOINT 220 XYVIEW 3 222 0.0 4.0 GRID 0 220 20 0 4 0.5 COLOUR 3 XLIMIT 3.0000 1.0000 YFROMO pep_flip.o ! MORE ! COLOUR 5 MRKTYP 0 box MRKSIZ 0.3 0.03 XLIMIT 3.0000 1.0000 YFROMO rs_fit_ave.o XLABEL Residue nr GTA Model M6 YLABEL RS-fit & Pep_flip values ! TEXT 50 3.5 10 'a rather high peak' TEXT 90 0.2 10 'a lowish one' ! END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! RSTATS statistics averaging ! NPOINT 14 COLOUR 2 XYVIEW 0.029 0.161 0 1 XLIMIT 0.03 0.01 XLABEL P212121 A2U - resolution bin (4(st/l)**2) - 930902 YLABEL CC & R before and after 5 averaging cycles; model M9A ! ! R-before = cat q | cut -c48-55 ! YVALUE * 0.285 ... 0.346 ! MORE YVALUE * 0.179 ... 0.254 ! ! CC-before = cat q | cut -c118-125 ! MORE COLOUR 3 YVALUE * 0.804 ... 0.529 ! MORE YVALUE * 0.910 ... 0.640 ! END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Wilson plot file #2: ! log<I2>/<I1> vs (sin(t)/l)**2 ! Produced by DATAMAN ! Filename = wilson_S1_S2_2.plt ! NPOINT 16 XLABEL (sin(theta)/lambda)**2 YLABEL log<I2>/<I1> MRKTYP 1 COLOUR 1 XYVIEW 0.0000E+00 4.5937E-02 3.5659E+00 4.1017E+00 XVALUE (1p,6e12.4) 1.2500E-03 3.7500E-03 6.2500E-03 8.7500E-03 1.1250E-02 1.3750E-02 1.6250E-02 1.8750E-02 2.1250E-02 2.3750E-02 2.6250E-02 2.8750E-02 3.1250E-02 3.3750E-02 3.6250E-02 3.8750E-02 4.1250E-02 4.3750E-02 ! YVALUE (1p,6e12.4) 2.5507E+00 3.2273E+00 3.7507E+00 3.6250E+00 3.8749E+00 3.8025E+00 3.7927E+00 3.8353E+00 3.8980E+00 3.9269E+00 3.9217E+00 3.8944E+00 3.9171E+00 3.9563E+00 3.9097E+00 3.9175E+00 ! MORE ! COLOUR 2 NPOINT 2 VALUES (1p,2e12.4) 1.2500E-03 3.5659E+00 4.3750E-02 4.1017E+00 ! END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by OOPS V. 940209/2.3 at Thu Feb 10 00:45:50 1994 for user gerard
NPOINT 290
XLABEL Residue number
YLABEL 1BYH_RESIDUE_RSC
COLOUR 2
XYVIEW 0.000 291.000 0.000 3.460
XLIMIT 1.000 1.000
YVALUE *
1.44130E+00 2.64300E-01 0.00000E+00 0.00000E+00 6.58700E-01
5.91000E-01 7.23400E-01 1.75690E+00 2.57700E-01 1.49100E+00
8.37900E-01 4.92900E-01 9.03400E-01 1.40620E+00 6.53700E-01
0.00000E+00 6.20500E-01 5.74200E-01 2.98340E+00 4.92700E-01
...
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
END
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by XPLO2D NPOINT 407 XYVIEW 0.00000 1.00000 0.10000 0.25000 XLIMIT 0.00000 0.00246 XLABEL Transl C-axis 0.0000 - 1.0000, 0.0025; file combi1_34.3dmatrix YLABEL TF values 0.1030 - 0.2210; ave 0.1590; sigma 0.0210 YVALUE (11f7.4) 0.1871 0.2027 0.2018 0.1832 0.1536 0.1251 0.1106 0.1160 0.1386 0.1687 0.1950 0.2078 0.2014 0.1758 0.1401 0.1111 0.1028 0.1186 0.1510 0.1861 0.2120 0.2215 0.2109 0.1829 0.1499 0.1281 0.1261 0.1427 0.1686 0.1926 0.2072 0.2078 0.1924 ... 0.1524 0.1716 0.1844 0.1861 0.1759 0.1572 0.1360 0.1199 0.1152 0.1238 0.1429 0.1660 0.1856 0.1956 0.1935 0.1809 0.1634 0.1478 0.1399 0.1425 0.1550 0.1738 0.1925 0.2028 0.1988 0.1811 0.1570 0.1350 0.1225 0.1237 0.1385 0.1624 0.1871 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- NPOINT 59 COLOUR 2 XYVIEW 1 59 0.15 0.35 XLIMIT 1 1 YFROMO rfree.o XLABEL Progress of XPLOR refinement YLABEL Rfree/Rnormal END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
REMARK Per-residue average distance
REMARK file produced by RMSPDB at Fri Aug 7 14:58:51 1992
REMARK Compared : janet1.pdb
REMARK and : janet3.pdb
REMARK
NPOINT 467
COLOUR 3
XLABEL Residue
YLABEL Average distance (A)
XVALUE (8f10.0)
9 10 11 12 13 14 15 16
...
465 466 467 468 469 470 471 472
473 474 475
YVALUE (8f10.4)
0.5985 0.4632 1.4046 0.5464 0.4185 0.3699 0.4425 0.3351
0.3912 0.4396 0.4540 0.4848 0.4675 0.3320 0.5120 0.4828
...
0.4233 0.5245 0.6107 0.4192 0.3084 0.3960 0.4020 0.5547
0.3876 0.5279 0.3319 0.4641 0.5340 0.3542 0.2966 0.8534
0.5287 0.2241 0.2335
END
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
REMARK Histogram file produced by RMSPDB at Fri Aug 7 14:58:51 1992
REMARK Compared : janet1.pdb
REMARK and : janet3.pdb
REMARK
NPOINT 11
COLOUR 3
XLABEL Distance intervals (A)
YLABEL Number of distances
XVALUE (1p,5e15.7)
0.0000000E+00 1.0000000E-01 2.0000000E-01 3.0000001E-01 4.0000001E-01
5.0000000E-01 6.0000002E-01 6.9999999E-01 8.0000001E-01 9.0000004E-01
1.0000000E+00
YVALUE (5f15.0)
20 123 302 424 389
265 170 90 49 35
0
END
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMARK Created by ODBMAN V. 001206/1.9.5 at Mon Dec 11 17:05:17 2000 for gerard REMARK Scatter plot of datablock (X) YEAR REMARK And datablock (Y) RFREE REMARK X ave,sdv,min,max = 1.9978E+03 1.3548E+00 1.9930E+03 2.0000E+03 REMARK Y ave,sdv,min,max = 2.5463E-01 3.8939E-02 6.7600E-02 4.6500E-01 REMARK X-Y corr. coeff., rmsd = -0.057 1.9975E+03 LINFIT NPOINT 5112 XLABEL Value of YEAR YLABEL Value of RFREE COLOUR 4 XYVIEW 1992 2001 0.0 0.5 MRKTYP 1 MRKSIZ 0.01 0.001 BOXPAR 1989.5 1 2000.5 XVALUE * 1.9960E+03 1.9970E+03 1.9990E+03 1.9960E+03 1.9980E+03 1.9960E+03 [...] 1.9980E+03 1.9990E+03 1.9980E+03 1.9980E+03 1.9990E+03 2.0000E+03 YVALUE * 3.2000E-01 4.2800E-01 2.8500E-01 4.5200E-01 3.1500E-01 3.5100E-01 [...] 1.5480E-01 1.2100E-01 1.0260E-01 1.4500E-01 1.3100E-01 9.4000E-02 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by XPLO2D V. 930728/0.9 at Wed Sep 1 17:01:38 1993 for user gerard
NPOINT 25
COLOUR 2
XYVIEW 0.10000 0.55000 0.00000 0.65000
XLABEL 1/Resolution (1/A)
YLABEL Luzzati plot WORKING data (R)
XVALUE *
0.120700 0.165837 0.192678 0.213220 0.230415 0.245399
0.258732 0.270636 0.281690 0.291971 0.301205 0.310078
0.318979 0.327332 0.335008 0.342466 0.349040 0.355872
0.362976 0.369004 0.374532 0.380228 0.386100 0.392157
0.397614
YVALUE *
0.418200 0.250400 0.198500 0.171300 0.186600 0.208700
0.223000 0.226000 0.229700 0.248300 0.241500 0.252100
0.264800 0.272900 0.304900 0.294000 0.289500 0.288000
0.311100 0.293800 0.325500 0.300900 0.331700 0.324900
0.312900
!
MORE
NPOINT 8
COLOUR 3
XVALUE *
0.150000 0.200000 0.250000 0.300000 0.350000 0.400000
0.450000 0.500000
YVALUE *
0.074000 0.098000 0.122000 0.145000 0.168000 0.191000
0.214000 0.237000
TEXT 0.505000 0.235000 10 '0.20'
!
MORE
NPOINT 9
COLOUR 4
XVALUE *
0.120000 0.160000 0.200000 0.240000 0.280000 0.320000
0.360000 0.400000 0.480000
YVALUE *
0.074000 0.098000 0.122000 0.145000 0.168000 0.191000
0.214000 0.237000 0.281000
TEXT 0.485000 0.279000 10 '0.25'
!
MORE
NPOINT 9
COLOUR 5
XVALUE *
0.133333 0.166667 0.200000 0.233333 0.266667 0.300000
0.333333 0.400000 0.466667
YVALUE *
0.098000 0.122000 0.145000 0.168000 0.191000 0.214000
0.237000 0.281000 0.319000
TEXT 0.471667 0.317000 10 '0.30'
!
MORE
NPOINT 10
COLOUR 6
XVALUE *
0.114286 0.142857 0.171429 0.200000 0.228571 0.257143
0.285714 0.342857 0.400000 0.457143
YVALUE *
0.098000 0.122000 0.145000 0.168000 0.191000 0.214000
0.237000 0.281000 0.319000 0.353000
TEXT 0.462143 0.351000 10 '0.35'
!
MORE
NPOINT 11
COLOUR 7
XVALUE *
0.125000 0.150000 0.175000 0.200000 0.225000 0.250000
0.300000 0.350000 0.400000 0.450000 0.500000
YVALUE *
0.122000 0.145000 0.168000 0.191000 0.214000 0.237000
0.281000 0.319000 0.353000 0.385000 0.414000
TEXT 0.505000 0.412000 10 '0.40'
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The contour routine expects data on an evenly spaced orthogonal 2D grid, so you can't specify X and Y values.
Ready-made 2D plot files are generated by:
- MAPMAN (section or slice of a map)
- LSQMAN (difference-distance matrix)
- MOLEMAN(2) (atom-atom distance plot)
- XPLO2D (2D translation function)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Keyword Format Type Rest of the line
-------------------------------------------------------------------------------
XPOINT (*) (I) nr of data points in the horizontal direction (note that
this is the number of intervals PLUS 1)
YPOINT (*) (I) nr of data points in the vertical direction (note that
this is the number of intervals PLUS 1)
XLIMIT (*) (2R) lower and upper values for X
YLIMIT (*) (2R) lower and upper values for Y
XLABEL (A) (A) label for marking the horizontal axis
YLABEL (A) (A) label for marking the vertical axis
NLEVEL (*) (I) the number of contour levels to plot
LEVELS --- --- the values of the contour levels; NLEVEL must be known;
the NLEVEL reals are read from the following records,
in free format
COLOUR --- --- the colours of the contour levels; NLEVEL must be known;
the NLEVEL integers are read from the following records,
in free format
RAMCOL (*) (6R) RGB values for the starting and the ending colour
used in colour-ramped 2D plots (r1 g1 b1 r2 g2 b2);
default is from blue to red
RAMLIM (*) (2R) limits on Z to determine the colour (default is
to use the entire dynamic range of ZVALUE)
RAMODE (A) (A) one of LIN(ear), LOG(arithmic) or ABS(olute);
the data (ZVALUE) will be transformed prior to
the colour-ramping takes place (the limits
provided with RAMLIM are updated as well !!)
RAMTYP (A) (A) type of ramping; one of HUE, SAT(uration), VAL(ue)
or WHI(te). HUE is the default, for ramping from
blue to red. SAT will enable ramping to or
from white. VAL enables ramping from black
to white or the other way around. WHI will
ramp from one colour to another and pass through
white in the middle.
ZVALUE (A) (A) the format for reading the XPOINT*YPOINT data values from
the following records; the values are reals, and they are
read with the X-index running fastest:
((ZVALUE(j,i),j=1,XPOINT),i=1,YPOINT)
NOTE: if the format is * then the data is read in free
format
LINE (*) (4R) X1,Y1, X2,Y2; draws line from (X1,Y1) to (X2,Y2)
BOX (*) (4R) XLO,XHI, YLO,YHI; draws a box
END --- --- stop reading; ignore the rest of the input file
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
!
! Example of a 2D plot file (Calpha distance plot)
!
REMARK Produced by MOLEMAN at Mon Aug 24 20:03:28 1992
REMARK From PDB file out.pdb
REMARK
XLABEL Residue
YLABEL Residue
NLEVEL 3
LEVELS
3.00 5.00 10.00
COLOUR
1 2 3
XPOINT 273
YPOINT 273
XLIMIT 1 273
YLIMIT 1 273
ZVALUE (7f10.1)
0.0 3.8 6.8 9.5 11.5 9.8 10.5
14.0 14.2 12.8 16.2 18.2 21.0 22.1
22.9 25.8 26.8 25.1 24.0 21.8 22.4
(...)
28.8 25.4 22.8 23.7 20.5 20.5 19.6
16.7 14.6 15.7 13.2 10.6 11.0 9.8
7.1 5.6 6.3 4.9 6.3 4.0 0.0
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by ODBM V. 931112/1.2 at Tue Nov 16 18:15:48 1993 for user gerard NLEVEL 6 LEVELS 0.09 0.093 0.096 0.099 0.102 0.104 COLOUR 8 9 10 11 12 13 XPOINT 16 YPOINT 16 XLABEL "direct translation search" CDHC 8-3A 931117 RF peak 14 YLABEL P21, a,c = 0 -> 0.5; 0.090/3/6/9 0.102/4 XLIMIT 0 0.5 YLIMIT 0 0.5 ZVALUE * 0.08762 0.07137 0.05669 0.07611 0.08157 0.07117 0.08299 0.08190 0.07753 0.07489 0.08262 0.08485 0.06363 0.07103 ... 0.07980 0.07093 0.07541 0.08553 0.07640 0.07573 0.08466 0.07419 0.08662 0.08762 0.07137 0.05669 0.07611 0.08157 0.07117 0.08299 0.08190 0.07753 0.07489 0.08262 0.08485 0.06363 0.07103 0.06756 0.08762 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by MAPMAN V. 931117/3.3 at Tue Feb 15 18:22:56 1994 for user gerard
NLEVEL 5
LEVELS
1.5 2.0 2.5 3 3.5
COLOUR
8 9 10 11 12
XLABEL Z-plane 100; horizontal = X-axis
YLABEL vertical = Y-axis; Z=1/2 Harker; PT/"AU" diff patt
XPOINT 21
YPOINT 21
XLIMIT 0.0000000E+00 0.5000000
YLIMIT 0.0000000E+00 0.5000000
ZVALUE (1p,6e13.4)
1.4791E-01 -7.5199E-02 -6.3337E-01 -1.0663E+00 -1.0237E+00 -9.9388E-01
-1.3477E+00 -1.1413E+00 3.5324E-01 1.8302E+00 1.7832E+00 9.5157E-01
7.2323E-01 5.8078E-01 -5.6884E-01 -2.0001E+00 -2.2918E+00 -1.6514E+00
...
8.9909E-01 3.9641E-01 2.7680E-01 8.5800E-01 8.3212E-01 2.2648E-01
6.6305E-02 3.8946E-03 -6.3404E-01 -1.2345E+00 -1.3464E+00 -1.3753E+00
-1.0769E+00 -6.0732E-02 6.0202E-01
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
These files are produced by DEJAVU. They may contain the following
keywords (all are in free format):
XYVIEW ... - viewport; must be the first card (xmin, xmax, ymin, ymax)
ALPHA ... - draw a cylinder (xmin, ymin, xmax, ymax, xwidth, text)
BETA ... - draw an arrow (xmin, ymin, xmax, ymax, xwidth, text)
END - end of file
At present, no comments etc. are allowed.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- XYVIEW -1.00 6.00 -0.50 1.50 BETA 0.00 0.00 0.00 1.00 0.80 'B1 ' BETA 1.00 1.00 1.00 0.00 0.80 'B2 ' ALPHA 2.00 0.00 2.00 1.00 0.80 'A1 ' ALPHA 3.00 1.00 3.00 0.00 0.80 'A3 ' BETA 4.00 1.00 4.00 0.00 0.80 'B4 ' BETA 5.00 0.00 5.00 1.00 0.80 'B3 ' ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use ODBM/ODBMAN (or manual file editing) to quickly create O-type datablock files (from XPLOR output, for example) for display with O2D !
BUGFIX - 930203 - labels for the axes could not be longer than 15 characters on the screen; this has been changed to 80 characters
BUGFIX - 930203 - sometimes the PostScript file wouldn't print; probable cause: use of "(" and ")" in axis labels; if the labels were longer than 40 characters, they were truncated which might result in an unmatched "(" in the PostScript file; remedy: length of the labels increased to 80 characters
Topology option: topology file produced by DEJAVU may be plotted and converted into PostScript with the TOPOLOGY option. Use a 2D window to plot the topology diagram in.
NAIVE - 930414 - a new option to quickly plot "O" datablock files. Just type NAIVE O_FILE (PS_FILE) after opening a 1D window and voila.
930419 - in 1D plot files, the format following XVALUE or YVALUE may now be * indicating free-format read.
* LEGENDS - all REMARK cards are now used to create a legend to your plot (maximum of 10 lines Times 12). Also, for 2D contour plots, (some of) the contour levels are included in this legend. Note that lines beginning with "!" in your plot file are real comment cards (i.e., they won't be echoed to the PostScript file).
* CONTOUR - a notorious and long-standing 'offset-bug' has been fixed in the 2D contour option.
* PIE CHARTS - new option
* There is a script in the OMAC directory to convert lots of plot files into PostScript format in one go (OMAC/o2dps). For example: $OMAC/o2dps 'x*.plt' 1d
The following colours are predefined:
0 = black
1 = red
2 = green
3 = yellow
4 = blue
5 = magenta
6 = cyan
7 = white
If you want other colours than this, edit the PostScript file (note that two commands have been defined for you already: C means "stroke setrgbcolour" and K means "stroke sethsvcolour").
Alternatively, you can use colour numbers 8 to 411 which have been defined as follows (in PostScript files only; on-screen on SGIs the colours are different):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- # 8 (light_grey ) = 852276012 RGB 0.800 0.800 0.800 # 9 (grey ) = 537395712 RGB 0.500 0.500 0.500 # 10 (dark_grey ) = 222515412 RGB 0.200 0.200 0.200 # 11 (white ) = 1062196212 RGB 1.000 1.000 1.000 # 12 (gainsboro ) = 917351274 RGB 0.862 0.862 0.862 # 13 (honeydew ) = 1000330169 RGB 0.941 1.000 0.941 # 14 (mistyrose ) = 938355700 RGB 1.000 0.894 0.882 # 15 (skyblue ) = 979160605 RGB 0.529 0.807 0.921 # 16 (light_steel_blue ) = 925643454 RGB 0.690 0.768 0.870 # 17 (lightcyan ) = 1062196090 RGB 0.878 1.000 1.000 # 18 (limegreen ) = 219987153 RGB 0.197 0.803 0.197 # 19 (yellowgreen ) = 219987559 RGB 0.603 0.803 0.197 # 20 (goldenrod ) = 145379170 RGB 0.854 0.647 0.126 # 21 (peru ) = 273176367 RGB 0.803 0.521 0.248 # 22 (light_salmon ) = 515506164 RGB 1.000 0.627 0.479 # 23 (medium_violet_red ) = 558989080 RGB 0.780 0.083 0.521 # 24 (snow4 ) = 576230957 RGB 0.545 0.537 0.537 # 25 (bisque2 ) = 765280177 RGB 0.933 0.835 0.717 # 26 (bisque3 ) = 662398767 RGB 0.803 0.717 0.619 # 27 (azure1 ) = 1062196153 RGB 0.941 1.000 1.000 # 28 (slateblue1 ) = 1061618189 RGB 0.513 0.436 1.000 # 29 (slateblue4 ) = 584311075 RGB 0.279 0.236 0.545 # 30 (skyblue1 ) = 1061998109 RGB 0.529 0.807 1.000 # 31 (lightskyblue3 ) = 855332404 RGB 0.552 0.713 0.803 # 32 (paleturquoise4 ) = 584627613 RGB 0.401 0.545 0.545 # 33 (cadetblue2 ) = 991836728 RGB 0.556 0.898 0.933 # 34 (aquamarine4 ) = 490255643 RGB 0.271 0.545 0.455 # 35 (springgreen2 ) = 499041292 RGB 0.000 0.933 0.463 # 36 (olivedrab1 ) = 269472508 RGB 0.752 1.000 0.244 # 37 (yellow2 ) = 13551537 RGB 0.933 0.933 0.000 # 38 (goldenrod3 ) = 132755247 RGB 0.803 0.607 0.114 # 39 (goldenrod4 ) = 95855149 RGB 0.545 0.412 0.079 # 40 (burlywood1 ) = 649928692 RGB 1.000 0.827 0.607 # 41 (orange3 ) = 13129519 RGB 0.803 0.521 0.000 # 42 (tomato3 ) = 247794479 RGB 0.803 0.310 0.224 # 43 (darkorchid2 ) = 991150790 RGB 0.698 0.228 0.933 # 44 (purple4 ) = 584173914 RGB 0.334 0.102 0.545 # 45 (mediumpurple2 ) = 991403643 RGB 0.623 0.475 0.933 # 46 (sgichartreuse ) = 478958024 RGB 0.444 0.776 0.444 # 47 (deep_sky_blue ) = 1061938188 RGB 0.000 0.749 1.000 # 48 (darkgreen ) = 12997644 RGB 0.000 0.393 0.000 # 49 (dark_khaki ) = 453732081 RGB 0.741 0.717 0.420 # 50 (wheat ) = 748538828 RGB 0.960 0.870 0.701 # 51 (dark_orange ) = 13158388 RGB 1.000 0.549 0.000 # 52 (coral ) = 342360052 RGB 1.000 0.499 0.314 # 53 (medium_purple ) = 912724556 RGB 0.576 0.440 0.858 # 54 (thistle ) = 901506907 RGB 0.847 0.749 0.847 # 55 (navajowhite3 ) = 584787759 RGB 0.803 0.701 0.545 # 56 (lemonchiffon1 ) = 855606260 RGB 1.000 0.980 0.803 # 57 (paleturquoise1 ) = 1062195945 RGB 0.733 1.000 1.000 # 58 (goldenrod2 ) = 153827249 RGB 0.933 0.705 0.134 # 59 (burlywood2 ) = 608977841 RGB 0.933 0.772 0.568 # 60 (tan4 ) = 190166573 RGB 0.545 0.353 0.169 # 61 (chocolate2 ) = 149385137 RGB 0.933 0.463 0.130 # 62 (brown4 ) = 157440557 RGB 0.545 0.138 0.138 # 63 (maroon1 ) = 747856884 RGB 1.000 0.204 0.701 # 64 (maroon2 ) = 698558385 RGB 0.933 0.189 0.654 # 65 (darkorchid1 ) = 1061421817 RGB 0.749 0.244 1.000 # 66 (mediumpurple1 ) = 1061693098 RGB 0.670 0.509 1.000 # 67 (thistle1 ) = 1062075380 RGB 1.000 0.882 1.000 # 68 (thistle2 ) = 991760305 RGB 0.933 0.823 0.933 # 69 (thistle3 ) = 855328559 RGB 0.803 0.709 0.803 # 70 (darkblue ) = 584069132 RGB 0.000 0.000 0.545 # 71 (sgilightblue ) = 801758711 RGB 0.491 0.619 0.752 # 72 (sgislateblue ) = 826745288 RGB 0.444 0.444 0.776 # 73 (navy_blue ) = 537931788 RGB 0.000 0.000 0.501 # 74 (medium_spring_green ) = 645890060 RGB 0.000 0.980 0.603 # 75 (olive_drab ) = 157868464 RGB 0.420 0.556 0.138 # 76 (darkgoldenrod ) = 59270877 RGB 0.721 0.525 0.044 # 77 (rosybrown ) = 600371949 RGB 0.737 0.560 0.560 # 78 (violetred ) = 604121915 RGB 0.815 0.126 0.564 # 79 (slateblue3 ) = 854960552 RGB 0.412 0.350 0.803 # 80 (deepskyblue2 ) = 991631372 RGB 0.000 0.698 0.933 # 81 (deepskyblue3 ) = 855219212 RGB 0.000 0.603 0.803 # 82 (deepskyblue4 ) = 584486924 RGB 0.000 0.408 0.545 # 83 (cadetblue4 ) = 584607058 RGB 0.326 0.525 0.545 # 84 (indianred1 ) = 449229812 RGB 1.000 0.416 0.416 # 85 (wheat4 ) = 433581613 RGB 0.545 0.495 0.401 # 86 (firebrick1 ) = 210970612 RGB 1.000 0.189 0.189 # 87 (lightsalmon2 ) = 482956209 RGB 0.933 0.584 0.448 # 88 (darkorange1 ) = 13107188 RGB 1.000 0.499 0.000 # 89 (dark_red ) = 12595757 RGB 0.545 0.000 0.000 # 90 (crimson ) = 260140906 RGB 0.862 0.079 0.236 # 91 (floralwhite ) = 1000309748 RGB 1.000 0.980 0.941 # 92 (mediumblue ) = 854601740 RGB 0.000 0.000 0.803 # 93 (dodger_blue ) = 1061748866 RGB 0.118 0.564 1.000 # 94 (steelblue ) = 752362783 RGB 0.275 0.509 0.705 # 95 (turquoise ) = 868083975 RGB 0.251 0.878 0.815 # 96 (medium_aquamarine ) = 711769501 RGB 0.401 0.803 0.666 # 97 (sea_green ) = 371766465 RGB 0.181 0.545 0.342 # 98 (lawngreen ) = 13607411 RGB 0.487 0.988 0.000 # 99 (green ) = 13619212 RGB 0.000 1.000 0.000 # 100 (lightyellow ) = 934269940 RGB 1.000 1.000 0.878 # 101 (brown ) = 185779859 RGB 0.647 0.165 0.165 # 102 (violet ) = 991438769 RGB 0.933 0.509 0.933 # 103 (medium_orchid ) = 880110309 RGB 0.729 0.334 0.827 # 104 (navajowhite4 ) = 400006701 RGB 0.545 0.475 0.369 # 105 (ivory1 ) = 1000330228 RGB 1.000 1.000 0.941 # 106 (honeydew4 ) = 551073293 RGB 0.513 0.545 0.513 # 107 (darkolivegreen3 ) = 383565447 RGB 0.635 0.803 0.353 # 108 (lightgoldenrod3 ) = 474732335 RGB 0.803 0.745 0.440 # 109 (darkgoldenrod1 ) = 75204596 RGB 1.000 0.725 0.059 # 110 (burlywood4 ) = 363281965 RGB 0.545 0.451 0.334 # 111 (wheat1 ) = 777934836 RGB 1.000 0.905 0.729 # 112 (chocolate3 ) = 132544303 RGB 0.803 0.401 0.114 # 113 (chocolate4 ) = 91516461 RGB 0.545 0.271 0.075 # 114 (pink2 ) = 769297329 RGB 0.933 0.662 0.721 # 115 (orchid4 ) = 575966765 RGB 0.545 0.279 0.537 # 116 (lightgreen ) = 604948032 RGB 0.564 0.933 0.564 # 117 (lightskyblue ) = 1041026589 RGB 0.529 0.807 0.980 # 118 (forestgreen ) = 153662610 RGB 0.134 0.545 0.134 # 119 (beige ) = 917451724 RGB 0.960 0.960 0.862 # 120 (deeppink ) = 616656884 RGB 1.000 0.079 0.576 # 121 (dark_orchid ) = 851658340 RGB 0.600 0.197 0.800 # 122 (peachpuff3 ) = 625666863 RGB 0.803 0.686 0.584 # 123 (dodgerblue4 ) = 584382539 RGB 0.063 0.306 0.545 # 124 (lightcyan4 ) = 584627691 RGB 0.479 0.545 0.545 # 125 (palegreen3 ) = 524074483 RGB 0.487 0.803 0.487 # 126 (indianred3 ) = 363162415 RGB 0.803 0.334 0.334 # 127 (indianred4 ) = 251904557 RGB 0.545 0.228 0.228 # 128 (salmon3 ) = 359076655 RGB 0.803 0.440 0.330 # 129 (salmon4 ) = 247782957 RGB 0.545 0.299 0.224 # 130 (lightsalmon4 ) = 284527149 RGB 0.545 0.342 0.259 # 131 (orangered2 ) = 12853169 RGB 0.933 0.251 0.000 # 132 (plum3 ) = 855204655 RGB 0.803 0.588 0.803 # 133 (antique_white ) = 897488864 RGB 0.980 0.921 0.843 # 134 (aliceblue ) = 1062167481 RGB 0.941 0.972 1.000 # 135 (khaki ) = 589187001 RGB 0.941 0.901 0.549 # 136 (lightgoldenrod ) = 547208113 RGB 0.933 0.866 0.509 # 137 (hot_pink ) = 752264180 RGB 1.000 0.412 0.705 # 138 (light_pink ) = 806049780 RGB 1.000 0.713 0.756 # 139 (antiquewhite4 ) = 507000365 RGB 0.545 0.513 0.471 # 140 (steelblue2 ) = 991607157 RGB 0.361 0.674 0.933 # 141 (turquoise3 ) = 855392268 RGB 0.000 0.772 0.803 # 142 (aquamarine1 ) = 884986367 RGB 0.499 1.000 0.831 # 143 (darkseagreen2 ) = 752797389 RGB 0.705 0.933 0.705 # 144 (darkseagreen3 ) = 649903723 RGB 0.607 0.803 0.607 # 145 (seagreen1 ) = 666882390 RGB 0.330 1.000 0.623 # 146 (springgreen4 ) = 297317388 RGB 0.000 0.545 0.271 # 147 (lightyellow4 ) = 515421741 RGB 0.545 0.545 0.479 # 148 (gold4 ) = 13065773 RGB 0.545 0.459 0.000 # 149 (rosybrown2 ) = 752564145 RGB 0.933 0.705 0.705 # 150 (indianred2 ) = 420890545 RGB 0.933 0.389 0.389 # 151 (sienna2 ) = 284663729 RGB 0.933 0.475 0.259 # 152 (brown2 ) = 256103345 RGB 0.933 0.232 0.232 # 153 (deeppink4 ) = 341889581 RGB 0.545 0.040 0.314 # 154 (magenta1 ) = 1061172212 RGB 1.000 0.000 1.000 # 155 (orchid1 ) = 1040726004 RGB 1.000 0.513 0.980 # 156 (sgibeet ) = 595829304 RGB 0.556 0.220 0.556 # 157 (sgi_teal ) = 596173032 RGB 0.220 0.556 0.556 # 158 (bisque ) = 818818036 RGB 1.000 0.894 0.768 # 159 (mint_cream ) = 1041224652 RGB 0.960 1.000 0.980 # 160 (slateblue ) = 854963628 RGB 0.416 0.353 0.803 # 161 (powderblue ) = 958261950 RGB 0.690 0.878 0.901 # 162 (light_sea_green ) = 711661706 RGB 0.126 0.698 0.666 # 163 (greenyellow ) = 207606450 RGB 0.678 1.000 0.185 # 164 (sienna ) = 198523519 RGB 0.627 0.322 0.177 # 165 (seashell2 ) = 925776817 RGB 0.933 0.898 0.870 # 166 (peachpuff2 ) = 724345777 RGB 0.933 0.796 0.678 # 167 (lemonchiffon2 ) = 798914481 RGB 0.933 0.913 0.749 # 168 (royalblue3 ) = 854983920 RGB 0.228 0.373 0.803 # 169 (lightsteelblue1 ) = 1062075172 RGB 0.792 0.882 1.000 # 170 (lightsteelblue2 ) = 991760109 RGB 0.737 0.823 0.933 # 171 (springgreen1 ) = 536858636 RGB 0.000 1.000 0.499 # 172 (chartreuse2 ) = 13551067 RGB 0.463 0.933 0.000 # 173 (red1 ) = 12596212 RGB 1.000 0.000 0.000 # 174 (deeppink2 ) = 575754161 RGB 0.933 0.071 0.537 # 175 (maroon4 ) = 416410157 RGB 0.545 0.110 0.385 # 176 (whitesmoke ) = 1020212172 RGB 0.960 0.960 0.960 # 177 (navajowhite ) = 724421620 RGB 1.000 0.870 0.678 # 178 (cornflowerblue ) = 987320725 RGB 0.393 0.584 0.929 # 179 (chocolate ) = 136749891 RGB 0.823 0.412 0.118 # 180 (maroon ) = 408102590 RGB 0.690 0.189 0.377 # 181 (snow3 ) = 839680815 RGB 0.803 0.788 0.788 # 182 (antiquewhite1 ) = 913233908 RGB 1.000 0.937 0.858 # 183 (navajowhite2 ) = 675078065 RGB 0.933 0.811 0.631 # 184 (steelblue1 ) = 1061909905 RGB 0.389 0.721 1.000 # 185 (lightskyblue2 ) = 991764111 RGB 0.643 0.827 0.933 # 186 (lightblue3 ) = 855372391 RGB 0.603 0.752 0.803 # 187 (turquoise2 ) = 991836172 RGB 0.000 0.898 0.933 # 188 (khaki4 ) = 333997613 RGB 0.545 0.525 0.306 # 189 (lightyellow3 ) = 752664367 RGB 0.803 0.803 0.705 # 190 (yellow1 ) = 13620212 RGB 1.000 1.000 0.000 # 191 (wheat2 ) = 728592305 RGB 0.933 0.847 0.682 # 192 (chocolate1 ) = 162004980 RGB 1.000 0.499 0.142 # 193 (brown1 ) = 276045812 RGB 1.000 0.251 0.251 # 194 (orange1 ) = 13258740 RGB 1.000 0.647 0.000 # 195 (orange2 ) = 13213617 RGB 0.933 0.603 0.000 # 196 (darkorange3 ) = 13006639 RGB 0.803 0.401 0.000 # 197 (lightpink4 ) = 429262381 RGB 0.545 0.373 0.397 # 198 (magenta3 ) = 854602543 RGB 0.803 0.000 0.803 # 199 (magenta4 ) = 584069677 RGB 0.545 0.000 0.545 # 200 (purple2 ) = 991094340 RGB 0.568 0.173 0.933 # 201 (purple3 ) = 854755831 RGB 0.491 0.150 0.803 # 202 (sgi_salmon ) = 478618388 RGB 0.776 0.444 0.444 # 203 (lavender_blush ) = 1020192756 RGB 1.000 0.941 0.960 # 204 (midnightblue ) = 474070127 RGB 0.099 0.099 0.440 # 205 (darkslateblue ) = 584315175 RGB 0.283 0.240 0.545 # 206 (cadet_blue ) = 670686593 RGB 0.373 0.619 0.627 # 207 (mediumseagreen ) = 478881016 RGB 0.236 0.701 0.444 # 208 (tan ) = 588986179 RGB 0.823 0.705 0.549 # 209 (darksalmon ) = 515466141 RGB 0.913 0.588 0.479 # 210 (light_coral ) = 538445753 RGB 0.941 0.501 0.501 # 211 (orange_red ) = 12873716 RGB 1.000 0.271 0.000 # 212 (pale_violet_red ) = 617026406 RGB 0.858 0.440 0.576 # 213 (darkviolet ) = 879768144 RGB 0.580 0.000 0.827 # 214 (snow2 ) = 970880945 RGB 0.933 0.913 0.913 # 215 (royalblue4 ) = 584326309 RGB 0.153 0.251 0.545 # 216 (dodgerblue3 ) = 855067755 RGB 0.095 0.455 0.803 # 217 (lightskyblue1 ) = 1062079166 RGB 0.690 0.886 1.000 # 218 (khaki2 ) = 559826865 RGB 0.933 0.901 0.521 # 219 (lightgoldenrod4 ) = 326637101 RGB 0.545 0.505 0.299 # 220 (sienna4 ) = 170167853 RGB 0.545 0.279 0.150 # 221 (darkorange4 ) = 12873261 RGB 0.545 0.271 0.000 # 222 (red3 ) = 12596015 RGB 0.803 0.000 0.000 # 223 (pink3 ) = 662246191 RGB 0.803 0.568 0.619 # 224 (magenta2 ) = 990917553 RGB 0.933 0.000 0.933 # 225 (mediumorchid2 ) = 991299391 RGB 0.819 0.373 0.933 # 226 (indigo ) = 546320691 RGB 0.295 0.000 0.509 # 227 (old_lace ) = 958346220 RGB 0.992 0.960 0.901 # 228 (peach_puff ) = 773688308 RGB 1.000 0.854 0.725 # 229 (light_slate_blue ) = 1061622289 RGB 0.517 0.440 1.000 # 230 (dark_olive_green ) = 207012186 RGB 0.334 0.420 0.185 # 231 (lightgoldenrodyellow ) = 876577760 RGB 0.980 0.980 0.823 # 232 (gold ) = 13459444 RGB 1.000 0.843 0.000 # 233 (orchid ) = 892801890 RGB 0.854 0.440 0.839 # 234 (bisque4 ) = 453500461 RGB 0.545 0.491 0.420 # 235 (cornsilk1 ) = 917464052 RGB 1.000 0.972 0.862 # 236 (honeydew2 ) = 934201210 RGB 0.878 0.933 0.878 # 237 (lightblue4 ) = 584594852 RGB 0.408 0.513 0.545 # 238 (olivedrab4 ) = 153662888 RGB 0.412 0.545 0.134 # 239 (khaki3 ) = 486298415 RGB 0.803 0.776 0.451 # 240 (sienna1 ) = 305670132 RGB 1.000 0.509 0.279 # 241 (brown3 ) = 222516015 RGB 0.803 0.200 0.200 # 242 (red2 ) = 12596145 RGB 0.933 0.000 0.000 # 243 (palevioletred3 ) = 576099119 RGB 0.803 0.408 0.537 # 244 (darkorchid3 ) = 854804071 RGB 0.603 0.197 0.803 # 245 (darkorchid4 ) = 584206756 RGB 0.408 0.134 0.545 # 246 (mediumpurple3 ) = 855020069 RGB 0.537 0.408 0.803 # 247 (mediumpurple4 ) = 584355193 RGB 0.365 0.279 0.545 # 248 (blanched_almond ) = 855545844 RGB 1.000 0.921 0.803 # 249 (moccasin ) = 756952052 RGB 1.000 0.894 0.709 # 250 (blue ) = 1061171212 RGB 0.000 0.000 1.000 # 251 (palegreen ) = 638554720 RGB 0.596 0.984 0.596 # 252 (chartreuse ) = 13619711 RGB 0.499 1.000 0.000 # 253 (salmon ) = 482871264 RGB 0.980 0.501 0.448 # 254 (pink ) = 848032756 RGB 1.000 0.752 0.796 # 255 (lavenderblush2 ) = 955116465 RGB 0.933 0.878 0.898 # 256 (lavenderblush3 ) = 822870831 RGB 0.803 0.756 0.772 # 257 (mistyrose4 ) = 519560749 RGB 0.545 0.491 0.483 # 258 (azure4 ) = 584627725 RGB 0.513 0.545 0.545 # 259 (skyblue2 ) = 991687163 RGB 0.495 0.752 0.933 # 260 (lightcyan3 ) = 855424717 RGB 0.705 0.803 0.803 # 261 (aquamarine2 ) = 827246043 RGB 0.463 0.933 0.776 # 262 (olivedrab2 ) = 252626633 RGB 0.701 0.933 0.228 # 263 (darkolivegreen1 ) = 474993444 RGB 0.792 1.000 0.440 # 264 (tomato1 ) = 305547252 RGB 1.000 0.389 0.279 # 265 (maroon3 ) = 604157743 RGB 0.803 0.161 0.564 # 266 (orchid3 ) = 839295791 RGB 0.803 0.412 0.788 # 267 (indigo2 ) = 440960142 RGB 0.130 0.533 0.408 # 268 (darkseagreen ) = 600553020 RGB 0.560 0.737 0.560 # 269 (palegoldenrod ) = 711878577 RGB 0.933 0.909 0.666 # 270 (lightsteelblue4 ) = 584564156 RGB 0.432 0.483 0.545 # 271 (chartreuse4 ) = 13153563 RGB 0.271 0.545 0.000 # 272 (darkolivegreen4 ) = 264811964 RGB 0.432 0.545 0.240 # 273 (coral1 ) = 367473652 RGB 1.000 0.448 0.338 # 274 (coral4 ) = 206832173 RGB 0.545 0.244 0.185 # 275 (lightpink2 ) = 724180913 RGB 0.933 0.635 0.678 # 276 (palevioletred4 ) = 395611693 RGB 0.545 0.279 0.365 # 277 (orchid2 ) = 970436529 RGB 0.933 0.479 0.913 # 278 (plum1 ) = 1061922804 RGB 1.000 0.733 1.000 # 279 (thistle4 ) = 584564269 RGB 0.545 0.483 0.545 # 280 (royalblue ) = 937861387 RGB 0.255 0.412 0.882 # 281 (medium_turquoise ) = 852294951 RGB 0.283 0.819 0.800 # 282 (cyan ) = 1062195212 RGB 0.000 1.000 1.000 # 283 (indian_red ) = 391501615 RGB 0.803 0.361 0.361 # 284 (antiquewhite3 ) = 736883503 RGB 0.803 0.752 0.690 # 285 (lemonchiffon4 ) = 474519085 RGB 0.545 0.537 0.440 # 286 (mistyrose2 ) = 876429233 RGB 0.933 0.835 0.823 # 287 (blue2 ) = 990916620 RGB 0.000 0.000 0.933 # 288 (steelblue3 ) = 855195970 RGB 0.310 0.580 0.803 # 289 (skyblue3 ) = 855267764 RGB 0.424 0.650 0.803 # 290 (lightcyan2 ) = 991872831 RGB 0.819 0.933 0.933 # 291 (turquoise4 ) = 584606732 RGB 0.000 0.525 0.545 # 292 (darkseagreen1 ) = 806343424 RGB 0.756 1.000 0.756 # 293 (yellow3 ) = 13418287 RGB 0.803 0.803 0.000 # 294 (gold3 ) = 13290287 RGB 0.803 0.678 0.000 # 295 (tan2 ) = 314154929 RGB 0.933 0.603 0.287 # 296 (firebrick2 ) = 194176945 RGB 0.933 0.173 0.173 # 297 (salmon1 ) = 445171700 RGB 1.000 0.549 0.412 # 298 (orange4 ) = 12957229 RGB 0.545 0.353 0.000 # 299 (plum4 ) = 584480301 RGB 0.545 0.401 0.545 # 300 (lightblue1 ) = 1062131449 RGB 0.749 0.937 1.000 # 301 (lightblue2 ) = 991812294 RGB 0.698 0.874 0.933 # 302 (turquoise1 ) = 1062154252 RGB 0.000 0.960 1.000 # 303 (lightyellow2 ) = 872335281 RGB 0.933 0.933 0.819 # 304 (yellow4 ) = 13153837 RGB 0.545 0.545 0.000 # 305 (coral3 ) = 297125679 RGB 0.803 0.357 0.271 # 306 (deeppink3 ) = 498151215 RGB 0.803 0.063 0.463 # 307 (hotpink1 ) = 752284660 RGB 1.000 0.432 0.705 # 308 (lightpink1 ) = 773512180 RGB 1.000 0.682 0.725 # 309 (mediumorchid4 ) = 584290795 RGB 0.479 0.216 0.545 # 310 (dark_cyan ) = 584627212 RGB 0.000 0.545 0.545 # 311 (ghostwhite ) = 1062167512 RGB 0.972 0.972 1.000 # 312 (seashell3 ) = 798769967 RGB 0.803 0.772 0.749 # 313 (peachpuff4 ) = 429358637 RGB 0.545 0.467 0.397 # 314 (cornsilk2 ) = 855533489 RGB 0.933 0.909 0.803 # 315 (cornsilk4 ) = 507020845 RGB 0.545 0.533 0.471 # 316 (ivory3 ) = 806141743 RGB 0.803 0.803 0.756 # 317 (honeydew3 ) = 806141696 RGB 0.756 0.803 0.756 # 318 (azure2 ) = 991872890 RGB 0.878 0.933 0.933 # 319 (cadetblue3 ) = 855392747 RGB 0.479 0.772 0.803 # 320 (darkseagreen4 ) = 445167016 RGB 0.412 0.545 0.412 # 321 (palegreen4 ) = 359183702 RGB 0.330 0.545 0.330 # 322 (springgreen3 ) = 433896460 RGB 0.000 0.803 0.401 # 323 (khaki1 ) = 600785908 RGB 1.000 0.964 0.560 # 324 (lightgoldenrod2 ) = 547204017 RGB 0.933 0.862 0.509 # 325 (goldenrod1 ) = 166462452 RGB 1.000 0.756 0.146 # 326 (firebrick3 ) = 170036015 RGB 0.803 0.150 0.150 # 327 (firebrick4 ) = 119654957 RGB 0.545 0.102 0.102 # 328 (orangered3 ) = 12817199 RGB 0.803 0.216 0.000 # 329 (mediumorchid3 ) = 854932173 RGB 0.705 0.322 0.803 # 330 (purple1 ) = 1061365355 RGB 0.607 0.189 1.000 # 331 (white ) = 1062196212 RGB 1.000 1.000 1.000 # 332 (black ) = 12595212 RGB 0.000 0.000 0.000 # 333 (paleturquoise2 ) = 991872694 RGB 0.682 0.933 0.933 # 334 (cadetblue1 ) = 1062154848 RGB 0.596 0.960 1.000 # 335 (cyan3 ) = 855424012 RGB 0.000 0.803 0.803 # 336 (green2 ) = 13550604 RGB 0.000 0.933 0.000 # 337 (burlywood3 ) = 528128815 RGB 0.803 0.666 0.491 # 338 (wheat3 ) = 629905199 RGB 0.803 0.729 0.588 # 339 (tomato2 ) = 284546993 RGB 0.933 0.361 0.259 # 340 (tomato4 ) = 170099245 RGB 0.545 0.212 0.150 # 341 (lightpink3 ) = 625526575 RGB 0.803 0.549 0.584 # 342 (palevioletred1 ) = 715663348 RGB 1.000 0.509 0.670 # 343 (palevioletred2 ) = 666345393 RGB 0.933 0.475 0.623 # 344 (firebrick ) = 153242310 RGB 0.698 0.134 0.134 # 345 (snow1 ) = 1041204212 RGB 1.000 0.980 0.980 # 346 (azure3 ) = 855424768 RGB 0.756 0.803 0.803 # 347 (slateblue2 ) = 991330795 RGB 0.479 0.404 0.933 # 348 (darkgoldenrod2 ) = 70962097 RGB 0.933 0.678 0.055 # 349 (darkgoldenrod3 ) = 63525679 RGB 0.803 0.584 0.048 # 350 (darkgoldenrod4 ) = 46556717 RGB 0.545 0.397 0.032 # 351 (tan1 ) = 338317300 RGB 1.000 0.647 0.310 # 352 (violetred1 ) = 629408756 RGB 1.000 0.244 0.588 # 353 (violetred2 ) = 588497841 RGB 0.933 0.228 0.549 # 354 (violetred3 ) = 506677039 RGB 0.803 0.197 0.471 # 355 (sgi_olive_drab ) = 243851832 RGB 0.556 0.556 0.220 # 356 (linen ) = 958326752 RGB 0.980 0.941 0.901 # 357 (lavender ) = 1041123217 RGB 0.901 0.901 0.980 # 358 (dark_turquoise ) = 872205324 RGB 0.000 0.807 0.819 # 359 (lavenderblush4 ) = 563623469 RGB 0.545 0.513 0.525 # 360 (seagreen2 ) = 621724990 RGB 0.306 0.933 0.580 # 361 (rosybrown4 ) = 445030957 RGB 0.545 0.412 0.412 # 362 (lightsalmon3 ) = 416814895 RGB 0.803 0.505 0.385 # 363 (mediumslateblue ) = 991334895 RGB 0.483 0.408 0.933 # 364 (blueviolet ) = 941807145 RGB 0.541 0.169 0.886 # 365 (seashell4 ) = 546858541 RGB 0.545 0.525 0.509 # 366 (steelblue4 ) = 584471776 RGB 0.212 0.393 0.545 # 367 (lightskyblue4 ) = 584564101 RGB 0.377 0.483 0.545 # 368 (paleturquoise3 ) = 855424600 RGB 0.588 0.803 0.803 # 369 (cyan2 ) = 991872012 RGB 0.000 0.933 0.933 # 370 (palegreen1 ) = 645911143 RGB 0.603 1.000 0.603 # 371 (lightgoldenrod1 ) = 585017332 RGB 1.000 0.925 0.545 # 372 (rosybrown3 ) = 649703215 RGB 0.803 0.607 0.607 # 373 (sienna3 ) = 247894831 RGB 0.803 0.408 0.224 # 374 (plum ) = 921304942 RGB 0.866 0.627 0.866 # 375 (lemonchiffon3 ) = 691831599 RGB 0.803 0.788 0.647 # 376 (ivory2 ) = 934201265 RGB 0.933 0.933 0.878 # 377 (rosybrown1 ) = 806093812 RGB 1.000 0.756 0.756 # 378 (salmon2 ) = 416819121 RGB 0.933 0.509 0.385 # 379 (darkorange2 ) = 13070257 RGB 0.933 0.463 0.000 # 380 (pink1 ) = 822822900 RGB 1.000 0.709 0.772 # 381 (papaya_whip ) = 889116660 RGB 1.000 0.937 0.835 # 382 (sandy_brown ) = 408567752 RGB 0.956 0.643 0.377 # 383 (mistyrose3 ) = 756770607 RGB 0.803 0.717 0.709 # 384 (royalblue1 ) = 1061645607 RGB 0.283 0.463 1.000 # 385 (royalblue2 ) = 991359251 RGB 0.263 0.432 0.933 # 386 (skyblue4 ) = 584519983 RGB 0.291 0.440 0.545 # 387 (chartreuse3 ) = 13417885 RGB 0.401 0.803 0.000 # 388 (darkolivegreen2 ) = 441370349 RGB 0.737 0.933 0.408 # 389 (hotpink2 ) = 698790833 RGB 0.933 0.416 0.654 # 390 (hotpink3 ) = 604378927 RGB 0.803 0.377 0.564 # 391 (hotpink4 ) = 416530989 RGB 0.545 0.228 0.385 # 392 (violetred4 ) = 350374445 RGB 0.545 0.134 0.322 # 393 (seashell ) = 991900660 RGB 1.000 0.960 0.933 # 394 (lightblue ) = 958230194 RGB 0.678 0.847 0.901 # 395 (pale_turquoise ) = 991872698 RGB 0.686 0.933 0.933 # 396 (burlywood ) = 568031090 RGB 0.870 0.721 0.529 # 397 (purple ) = 999434879 RGB 0.627 0.126 0.941 # 398 (antiquewhite2 ) = 852351921 RGB 0.933 0.874 0.800 # 399 (ivory4 ) = 551073325 RGB 0.545 0.545 0.513 # 400 (seagreen3 ) = 538754323 RGB 0.263 0.803 0.501 # 401 (green4 ) = 13153292 RGB 0.000 0.545 0.000 # 402 (gold2 ) = 13403057 RGB 0.933 0.788 0.000 # 403 (coral2 ) = 342274993 RGB 0.933 0.416 0.314 # 404 (pink4 ) = 457590317 RGB 0.545 0.389 0.424 # 405 (plum2 ) = 991615921 RGB 0.933 0.682 0.933 # 406 (cornsilk3 ) = 741110575 RGB 0.803 0.784 0.694 # 407 (dodgerblue2 ) = 991454330 RGB 0.110 0.525 0.933 # 408 (lightsteelblue3 ) = 855328391 RGB 0.635 0.709 0.803 # 409 (green3 ) = 13417484 RGB 0.000 0.803 0.000 # 410 (orangered4 ) = 12745261 RGB 0.545 0.146 0.000 # 411 (mediumorchid1 ) = 1061582714 RGB 0.878 0.401 1.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(1) Most READ statements don't have error traps which causes the program to crash in case of a read error.
(2) Interactive graphics only works for the SGI version.
Created at Thu Jan 18 19:16:52 2007
by MAN2HTML version 070111/2.0.8 . This manual
describes O2D, a program of the Uppsala
Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2007.