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
- For dotstyle=0, no signs are drawn at the data points
- If dotstyle=1 plus-signs are used.
- If dotstyle=2 x-signs are used.
- If dotstyle=3 squares are used.
- If dotstyle=4 diamonds are used.
- If dotstyle=5 upright triangles are used.
- If dotstyle=6 uside-down triangles are used.
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.