Sample data and sample PostScript output may be found in
the directory $RIBBONS_HOME/analysis/plot.
bf-ps
rsr-ps
rms-ps
geom-ps
dihe-ps
surf-ps
sig-ps
The ribbon-errors script produces ASCII lists
of per-residue information.
These *.list files are my ''standard''
per residue listing of output.
All consist of a required 3-line header, followed by lines of:
res# res-name value-res value-mc value-sc.
The default plotting action uses only the res# and values of
mainchain (mc) and sidechain (sc).
The mc values are shown on top of the X-axis and sc values
mirrored below, with the residue number scale below that.
Options allow one to change this behavior.
All of these programs have the following usage:
xxx-ps [options] ascii.list > output.ps
Options are:
-
-t "Your title string"
This must be in quotes if the title is more than one word.
Default title is taken from the list file.
To eliminate the title, use: -t ""
- -s Xsize.inch,Ysize.inch
The default is: -s 5.0,1.5
Please note: !! No space allowed before/after the comma !!
Please note: !! This size if for the data axes only !!
It doesn't take labels into account.
There is always about 1 inch of labeling to the left
of the ''origin'', and about 1/4 inch above and below.
- -o Xorigin.inch,Yorigin.inch
The default is: -o 2.0,5.5 which centers on a standard page.
The origin is the point where the X-axis meets the Y-axis,
which is different for a ''-2'' or a ''-1'' plot (see below).
- -2 res | mc | sc,res | mc | sc
The default behavior is: -2 mc,sc
which plots mainchain values on top, sidechain on bottom.
These are the literal strings 'res' or 'mc' or 'sc'.
Again, no space is allowed between the strings and comma.
These ''mirror'' plots always assume positive values only,
true for the ''bf'', ''rsr'', ''shift'', ''geom'',
and ''dihe'' data.
This option should not be chosen with a Sigma plot.
- -1 res | mc | sc
The default is automatically set to ''res''
if doing a sigma plot.
- -m max.value
The default is determined from data.
This is used to set a common scale. For example,
if one set of data has a maximum B-factor of 50,
and another a maximum of 30, each plot will have
a different scale factor along Y.
Use -m 50.0 to force each to be on the same scale.
-
-d
Put the tick marks/labels for residue axis pointing down.
The default points them up, which may overlap with your
data if the Ysize is small.
For ''-1'' plots, they are always down.
Secondary Structure Cartoons
A representation of the linear sequence in terms of
helix, sheets, and everything else may be generated
from a ribbons *.ss file.
This will usually be used in conjunction with the
per-residue plots above.
The options are the same as above, but only the ''-o'' and
''-s'' make any sense:
ss-ps [options] ribbons.ss > output.ps
Ramachandran Plots
Another class of plots are generated from the output of
pdb-pro-ss and pdb-chi-ss
(which are automatically called by ribbon-errors .)
These produce ascii lists which include information on the dihedral
angles for each residue.
The ''rama'' plot has circles for each amino acid except glycine,
which is marked by a diamond. Allowed regions are shaded
according to probability. The lightest regions are allowed
only for glycine. The ''chis'' give ramachandran-like plots
for each amino acid type.
They are generated as follows:
rama-plot < ascii_list.rama > rama.ps
rama-plot "Your title string" < ascii_list.rama > rama.ps
chis-plot < ascii_list.chis > chis.ps
Luzzati Plots
A commonly used error analysis technique is the Luzzati plot.
The input 'luzzati_error.plot' is generated by CNS example script
'./inputs/xtal_refine/model_stats.inp'.
(See the example file and Read.Me in $RIBBONS_HOME/analysis/plot/).
Use as follows:
luz-plot [luzOptions] luzzati_error.plot > luz.ps
Ribbons User Manual / UAB-CBSE / carson@uab.edu