SCATTER-V2 options

This file contains all of the options of SCATTER V2 in random order, without any structure. Refer to the main help file for a better guide.

SECSTR

Syntax:
SECSTR integer
Specifies the column where the secondary structure can be found. This makes a secondary structure plot, assuming that all residues are given in order, and secondary structure is given as 'H'/'3' for helix, 'S'/'E' for strand, and any other symbol for coil and loop. Works best if all Y values for all points are equal.

XSIXTY

Syntax:
XSIXTY
Change the ticks at the X axis such that 60's are longer instead of 5's. This makes it easier to recognise nice angles.

YSIXTY

Syntax:
YSIXTY
Change the ticks at the Y axis such that 60's are longer instead of 5's. This makes it easier to recognise nice angles.

APPEND

Syntax:
APPEND
If this option is specified, no new Xfig file is created. Instead, the new information is appended to one that already exists.

NOPUB

Syntax:
NOPUB
Misnomer. If this option is specified, the axis divisions are left out of the plot (No Publication...)

NOTITLE

Syntax:
NOTITLE
If this option is specified, the title of the plot containing information about username, time, input file, and number of data points is omitted from the output.

RANK

Syntax:
RANK
Specify that a rank correlation should be calculated. Which values are calculated is dependent on the size of the data set. Many values are followed by a Prob: the probability that this level of correlation is reached for a random data set of the same size.

NOAX

Syntax:
NOAX
Specify that the axes should not be extended to make nice round numbers at the ends.

FULLNUM

Syntax:
FULLNUM
Specify that the numbers at the ends of the axes should not be divided by a suitable power of 10, but instead used verbatim.

AXDIV

Syntax:
AXDIV integer
Maximum number of divisions on the axes. This has influence on the maximum numbers at the end of the axes and the power of 10 used to divide them.

REVX

Syntax:
REVX
Specifies that the X-axis should be reversed. that is: the numbers along the X axis should run from high to low.

REVY

Syntax:
REVY
Specifies that the Y-axis should be reversed. that is: the numbers along the Y axis should run from high to low.

SPACE

Syntax:
SPACE float
Percentage of extra space to allow at all 4 ends of the plot.

ERX

Syntax:
ERX float
Fixed standard deviation in all X coordinates.

RHO

Syntax:
RHO float
Correlation between the standard deviation in X and the standard deviation in Y. Needed for a robust fit, default set at 0.0

ERY

Syntax:
ERY float
Fixed standard deviation in all Y coordinates.

NSDX

Syntax:
NSDX integer
Alternative:
SDX
Number of the column in the input file where the standard deviation in the X coordinate can be found. Default: no standard deviation in X.

XMOD

Syntax:
XMOD float
Specify that values of X=X0 and X=X0+float are actually identical (like 1 and 25 hours on a clock). If the FOLD option is not given, scatter will change the data read such that any two subsequent points are less than MOD/2 apart. So: if you are reading a sequence of torsion angles using 'XMOD 360', and the values in subsequent lines are '178 179 179.5 -179 179', scatter will plot the values as '178 179 179.5 181 179' too keep the values as close together as possible.

YMOD

Syntax:
YMOD float
Specify that values of Y=Y0 and Y=Y0+float are actually identical (like 1 and 25 hours on a clock). If the FOLD option is not given, scatter will change the data read such that any two subsequent points are less than MOD/2 apart. So: if you are reading a sequence of torsion angles using 'XMOD 360', and the values in subsequent lines are '178 179 179.5 -179 179', scatter will plot the values as '178 179 179.5 181 179' too keep the values as close together as possible.

FOLD

Syntax:
FOLD
Tell SCATTER to try and FOLD the X and Y values, such that all X values are between -XMOD/2 and XMOD/2 and all Y values between -YMOD/2 and YMOD/2

SAMELENGTH

Syntax:
SAMELENGTH
Make all ticks along the axes equal sized.

ROBUST

Syntax:
ROBUST
Perform a robust fit, taking standard deviations in X into account.

NSDY

Syntax:
NSDY integer
Alternative:
SDY
Number of the column in the input file where the standard deviation in the Y coordinate can be found. Default: no standard deviation in Y.

SX

Syntax:
SX float
When determining the scale of the plot, SX is used instead of the lowest X value. Values thus falling outside the plot will be "clipped".

SY

Syntax:
SY float
When determining the scale of the plot, SY is used instead of the lowest Y value. Values thus falling outside the plot will be "clipped".

SR

Syntax:
SR float
When determining the scale of the plot, SR is used instead of the lowest R value. Values thus falling outside the plot will be "clipped".

EX

Syntax:
EX float
When determining the scale of the plot, EX is used instead of the highest X value. Values thus falling outside the plot will be "clipped".

EY

Syntax:
EY float
When determining the scale of the plot, EY is used instead of the highest Y value. Values thus falling outside the plot will be "clipped".

DX

Syntax:
DX float
When determining the scale of the plot, SX+DX is used instead of the highest X value. Values thus falling outside the plot will be "clipped".

DY

Syntax:
DY float
When determining the scale of the plot, SY+DY is used instead of the highest Y value. Values thus falling outside the plot will be "clipped".

CSL

Syntax:
CSL
Copy selected lines to output file 45. This file will normally be called fort.45

LSQ

Syntax:
LSQ
Perform least squares fit without drawing the line.

SCUMAV

Syntax:
SCUMAV float
Rescale the plot to the cumulative average +/- float.

LCUMAV

Syntax:
LCUMAV

TIC

Syntax:
TIC
Specifies that the first line of the datafile contains one-word names for each of the columns in the data.

TEX

Syntax:
TEX
Give the powers of 10 in the axis labels as LaTeX math environments.

FFT

Syntax:
FFT
Perform a FFT on the data. Requires that you use 0 for NX. Automatically extends the data with ample 0.0 values at both ends to get a proper frequency spectrum.

PFFT

Syntax:
PFFT
Perform a periodic FFT on the data. Requires that you use 0 for NX, and needs a power of 2 as the number of data points. No extention of the data at either end is performed.

ACF

Syntax:
ACF
Calculate the auto correlation function of the data. Requires that you use 0 for NX.

NOTEXT

Syntax:
NOTEXT
Show no text at all in the plot.

CUMAV

Syntax:
CUMAV
Calculate cumulative averages.

CUMSUM

Syntax:
CUMSUM
Calculate cumulative sums.

THOR

Syntax:
THOR
Typeset all text horizontally. Without this option, the text along the Y axis will be rotated by 90 degrees.

LSQL

Syntax:
LSQL
Calculate a linear least squares fit, and draw a line representing the fit.

POLY

Syntax:
POLY integer
Calculate a polynomial least squares fit of order integer, and draw a line representing the fit.

LOGX

Syntax:
LOGX
Take the log of the X values before drawing. Use LOGLOG if you want LOGX LOGY

LOGY

Syntax:
LOGY
Take the log of the Y values before drawing. Use LOGLOG if you want LOGX LOGY

LOGR

Syntax:
LOGR
Take the log of the R values before drawing.

ABSX

Syntax:
ABSX
Calculate X=ABS(X) when reading the data.

ABSY

Syntax:
ABSY
Calculate Y=ABS(Y) when reading the data.

ABSR

Syntax:
ABSR
Calculate R=ABS(R) when reading the data.

LOGLOG

Syntax:
LOGLOG
Identical to LOGX LOGY: double log scales.

SORTX

Syntax:
SORTX
Sort all values increasing in X value.

SHRINK_SQUARE

Syntax:
SHRINK_SQUARE
Make the XMAX and YMAX equal to MIN(XMAX,YMAX) and XMIN and YMIN equal to MAX(XMIN,YMIN).

EXTEND_SQUARE

Syntax:
EXTEND_SQUARE
Make the XMAX and YMAX equal to MAX(XMAX,YMAX) and XMIN and YMIN equal to MIN(XMIN,YMIN).

TORSR

Syntax:
TORSR
Treat the R value as a torsion angle, and display a "+" "-" or "square" sign depending on whether the torsion angle is "+gauche", "-gauche" or "trans", respectively.

SPLINE

Syntax:
SPLINE
Alternative:
SPLIN
Draw a spline through the points instead of straight lines. Use NSP to specify interpolation factor.

LINESTYLE

Syntax:
LINESTYLE integer
Alternative:
LIN
Draw a line connecting the points.

NSP

Syntax:
NSP integer
Interpolation factor for SPLINE. Default value is 10

DOTSTYLE

Syntax:
DOTSTYLE integer
Alternative:
DOT
the default dotstyle is 1. See also LINESTYLE.

INTERVAL

Syntax:
INTERVAL integer
Draw only a sign for one every integer data points.

NDOT

Syntax:
NDOT integer
Alternative:
ND
Specifies the number of the column in the datafile where the dot-type can be found. See DOTSTYLE for the dot-types.

PEAK

Syntax:
PEAK integer
Specifies the number of peaks [Maxima in the function Y=F(X)] to determine in the final graph.

TEXT

Syntax:
TEXT
Alternative:
TE text
Give a name to the plot.

XTEXT

Syntax:
XTEXT text
Name the X axis.

YTEXT

Syntax:
YTEXT text
Name the Y axis.

ZTEXT

Syntax:
ZTEXT floatx floaty text
Alternative:
TEZ
Put a text-string in the plot area. floatx,floaty are a coordinate pair, where 0,0 is the lower left corner of the plot, and 1,1 the top right.

ER

Syntax:
ER float
When determining the scale of the plot, ER is used instead of the highest R value. Values thus falling outside the plot will be "clipped".

DR

Syntax:
DR float
When determining the scale of the plot, SR+DR is used instead of the highest R value. Values thus falling outside the plot will be "clipped".

RADMAX

Syntax:
RADMAX float
Alternative:
RM
The maximum radius to use for the symbols if the symbol-size is to be dependent on NR. Default 0.30 cm

NPLX

Syntax:
NPLX integer
Number of plots in the X direction that will be on the page. See IPL. Default 1.

NPLY

Syntax:
NPLY integer
Number of plots in the Y direction that will be on the page. See IPL. Default 1.

IPL

Syntax:
IPL integer
The sequence number of the plot. Between 1 and NPLX times NPLY. Default 1.

NX

Syntax:
NX integer
The number of the column in the datafile where X can be found. If 0, the linenumber in the file is used as the X coordinate.

NY

Syntax:
NY integer
The number of the column in the datafile where Y can be found. If 0, the linenumber in the file is used as the Y coordinate.

HI

Syntax:
HI float
The total height of the page in cm.

WI

Syntax:
WI float
The total width of the page in cm

MARGIN

Syntax:
MARGIN float
Alternative:
MARG
The percentage of white space to reserve for text around the actual plotting area.

RAD

Syntax:
RAD float
Alternative:
RA
The size of the symbols used in cm. Default 0.05.

NR

Syntax:
NR integer
The number of the column in the input file where the R coordinate is to be found. If 0, the linenumber in the file is used as the Y coordinate.

SMOOTH

Syntax:
SMOOTH integer
The number of successive datapoints to average to get a more smooth appearance of a saw-tooth plot. This does reduce the number of datapoints by integer-1. Default 1.

AVER

Syntax:
AVER integer
The number of successive datapoints to average to reduce the total number of points. This will reduce the number of datapoints by a factor of integer. Default 1.

X=0

Syntax:
X=0
Draw the line X=0 into the plotting area.

X=

Syntax:
X= float
Draw the line X=float into the plotting area.

Y=0

Syntax:
Y=0
Draw the line Y=0 into the plotting area.

Y=

Syntax:
Y= float
Draw the line Y=float into the plotting area.

Y=X

Syntax:
Y=X
Draw the line Y=X into the plotting area.

Y=-X

Syntax:
Y=-X
Draw the line Y=-X into the plotting area.

NC

Syntax:
NC integer relation float
Specify a numeric constraint on the datafile. Only lines satisfying this numeric constraint will be used to collect datapoints and to write to a file if CSL is active.

The integer is the column number to be constrained.

The relation is "<" ">" "<>" or "=" (or the fortran like LT, GT, NE, EQ). The float is the comparison value.

Example: "NC 4 LT 5.0" will only select those lines that have the number in column 4 less than 5.0.

CC

Syntax:
CC integer relation text
Specify a character constraint on the datafile. Only lines satisfying this numeric constraint will be used to collect datapoints and to write to a file if CSL is active.

The integer is the column number to be constrained.

The relation is "<" ">" "<>" or "=" (or the fortran like LT, GT, NE, EQ). The text is the comparison value.

Example: "CC 4 LT FFF" will only select those lines that have the string in column 4 less than FFF, when compared in ASCII.

FILE

Syntax:
FILE name
Alternative:
FI
Specify the name of the input-file. ".dat" will be appended if no extension is given.

OUTFILE

Syntax:
OUTFILE name
Alternative:
OUTFI
Specify the name of the fig-file. ".fig" will be appended if no extension is given.