Program : O2D
Version : 990206
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
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
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://alpha2.bmc.uu.se/usf/factory_8.html]
* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
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
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 and pie-charts
(d) 2D contour plots (e.g., CA-CA distance plots or map sections)
(e) 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 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 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 -----
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.
----- 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
# 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 -----
! 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.
----- 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
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 -----
The executable for Silicon Graphics machines lives in: /nfs/public/IRIX/bin and is called 4d_o2d.
If there are specific options or features you would like to see in this program, let me know.
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.
* COLOUR - from version 4.0 onward, simple colour PostScript
is used. As on SGIs, colours 0 to 7 are defined:
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").
* 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
(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 Wed Feb 24 01:44:11 1999
by MAN2HTML version 971024/1.6