2.36 ******************
* CTOUR WRITE-UP *
******************
CTOUR is a program to create contoured plots of electron density
maps which can then be displayed or printed. The program accepts an
input map which is prepared by FSFOUR in the default orientation
(NORN=0), along with limit, direction and contouring information.
The output consists of one or more generic metafiles which can be
converted to the format needed for a given display by the appropriate
driver program, several of which are provided. Multiple plots can be
created within a single run, with each plot consisting of either an
individual map section, a mono projection over multiple sections, or a
stereo projection over multiple sections. Any map region may be
selected and viewed down either a direct cell axis or a reciprocal
cell axis (the latter used for projections). The metafiles created
will have the names plt001.plt, plt002.plt etc and can be viewed
via the driver programs VIEWPLT or VIEWPLT_X (on SGI or X-window
supporting workstations), by PLTTEK (on terminals supporting TEKTRONIX
4010 graphics) or converted to PostScript for subsequent printing
by MKPOST. Note that in general program MAPVIEW (or MAPVIEW_X) would
be preferred to examine contoured plots, since it allows the
interactive selection (and modification) of orientation, region and
contouring intervals. In some instances CTOUR has advantages however,
as it facilitates creation of hard copies for examination away from the
terminal or workstation, for creation of minimaps, and for stereo
plots. CTOUR is very useful for examination of difference Patterson
maps, where for example, all of the Harker sections can be generated
and then displayed simultaneously with the program VIEWPLT (or
VIEWPLT_X). It is recommended that one first examine the plots with
VIEWPLT or VIEWPLT_X before converting to PostScript as this can
be done extremely rapidly, whereas printing and even simply
displaying PostScript files can be much more time consuming.
INPUT DATA (UNIT 5)
CARD I MAPFIL (free format)
MAPFIL = Input map file (from FSFOUR, in default
orientation i.e. NORN=0)
CARD II CMIN,CMAX,CSTEP,IGRID,PSIZE,VDIS,RSCALE (free format)
CMIN =
Minimum, maximum and increment for contour
CMAX =
levels, on the scale set by RSCALE (see below)
CSTEP =
IGRID = 0 To include labels and border on plots
= 1 To include labels, border and grid lines on
plots (facilitates coordinate measurment for
Pattersons)
= 2 To eliminate labels, grid lines and border on
plots
PSIZE = Plot size in inches (usually 10. if hard copy
is to be produced).
VDIS = View distance in inches (usually 30., used
only for stereo plots. Decreasing it increases
the stereo effect).
RSCALE = Sets density scale for contours. If 0., then
density is scaled such that the largest value
in the unit cell is 999. If > 0., then the
density is on an absolute scale (minus the
F000/V term) when the F's used in map creation
are related to an absolute scale by the
factor RSCALE, i.e when F(abs)=RSCALE*F(input).
Regardless of the choice, the min, max and
sigma for the map on the chosen scale will be
listed on the output, and can be used to set
contour levels for a subsequent run.
**** The following card can be repeated as many times as desired ****
CARDS III NSEC,XMN,XMX,YMN,YMX,ZMN,ZMX,NORN (free format)
NSEC = 0 for individual sections, one plot per
section
= 1 for mono projection, one plot for entire
range
= 2 for stereo projection, one plot for
entire range
XMN =
XMX =
YMN = Minimum, maximum coordinates (fractional)
in a, b and c directions defining map
YMX = volume to be contoured.
ZMN =
ZMX =
NORN = 1 view as YZ sections (look down a or a*)
= 2 view as XZ sections (look down b or b*)
= 3 view as XY sections (look down c or c*)
************** EXAMPLES **************
1) The following script will compute a Patterson map and contour
three Harker sections. Three generic plot files (having the
names pltNNN.plt where NNN is a three digit number) will be
created. We start contouring at about 3% of the origin peak
height, which will be scaled to 999. and increase in steps
of 1% of the origin peak. We request that labels and a grid
are included to facilitate coordinate measurement. Finally,
we convert the generic plot files to Postscript. The
corresponding PostScript files will have the names pltNNN.pst
#compute the difference Patterson map
#
fsfour << eod > fsfour.l
seb.pam
Difference Patterson, 3A
0 48 72 80 5 0 20 0 0 0 0.
patt.ref
patt.map
eod
#
#now contour three Harker sections
#
ctour << eod2 > ctour.l
patt.map
30. 999. 10. 1 10. 30. 0.
0 0.5 0.5 0.0 1.0 0.0 1.0 1
0 0.0 1.0 0.5 0.5 0.0 1.0 2
0 0.0 1.0 0.0 1.0 0.5 0.5 3
eod2
#
#now convert all generic plot files to PostScript
#
mkpost *.plt
#
2) The following script will compute an MIR map and generate
a series of plots. First a small mono projection down the b*
axis is created. Then a minimap is made, contouring
individual sections. We start contouring at one sigma
and increase to the maximum in steps of sigma. Min, max
and sigma values were obtained from the log from a prior
short run which contoured only a single section. Labels
and a border are requested, but no grid lines. Finally,
all generic plot files are created to PostScript.
#compute the solvent flattened MIR map
#
fsfour << eod > fsfour.l
pdc.pam
PDC MIR MAP, 3A
0 144 80 120 1 0 20 0 0 0 0.
phi16cy.31
mir.map
eod
#
#now contour both a projection and individual sections
#
ctour << eod2 > ctour.l
mir.map
146. 999. 146. 0 10. 30. 0.
1 -.5 .5 -.05 .05 -.5 .5 2
0 -.42 .45 -.45 .42 -.08 .56 2
eod2
#
#now convert all generic plot files to PostScript
#
mkpost *.plt
#