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22.4 2DPLOT Command — Make a Scatter Plot

22.4.1 Syntax

     2DPLOT [ CODE  ] [UNIT unit-number] [TITLE string del]
            [NUMBER ]
            [VERTICAL range] [HORIZ range]

Syntactic ordering: The first option must appear first in the command.

22.4.2 Function

This command is used for plotting the second selection as a function of the first selection. Each selection has residue numbers and position numbers associated with each point. These numbers can serve as identifiers for the data points making it possible to relate the data points in two selections and produce matched pairs of data points. Plots of these pairs can be used to demonstrate correlations or patterns between the two selections (for example phi-psi or Ramachandran plots).

The first option in the command determines whether matching will be done by residue number or sequence number. If all of the data in both selections is uniquely identified by the specified identifier then a rapid algorithm is used to match the data. If the data is not uniquely identified then the match will use the order of occurrence in selections to resolve ambiguities. For example if the first selection was generated by selecting all dihedral angles, then the selection will be unique by sequence number but not unique by residue. If the second selection also contained all of the dihedrals from a second structure, it would not be unique by residue either. If NUMBER is specified then the two lists, then a unique mapping of one selection onto the other exists (although if the sequences of the two structures were different it may not be the desired mapping). Conversely, RESIDUE will result in multiple possible matchings of which one must be chosen to produce a plot.

The routine resolves this ambiguous mapping situation by matching the first available data for a residue (or number) in selection one with and first available data for the same residue (or number) in the second selection. In the example above RESIDUE mapping will align the first dihedrals of each residue etc. If a sequence mismatch exists between the structures and the mismatched residues contain different numbers of dihedrals, then for that residue pair the first dihedral will be matched with the first and so forth until all of the dihedrals in one residue are matched. Note that the extra data will now be ignored rather than offsetting all subsequent matches. NUMBER mapping would align the first dihedral in each structure etc., but would misalign all of the data past the mismatch.

CODE results in residue matching and the use of one letter amino acid codes for plot symbols. The default for the first option is RESIDUE.

The x (horizontal) axis is used for numbers from the first selection; the y (vertical) axis is used for number from the second selection.

If UNIT is specified, the pairs are output to the unit and no printer plot is made. Otherwise, the plot goes on the printer.

TITLE gives a title that appears at the top of plot.

VERTICAL and HORIZ can be used to specify the vertical and horizontal ranges and sizes of the plot. If unspecified, the limits will be set to the minimum and maximum in the data and the number of columns will set as large as will fit on a line. If specified, the first two numbers give the limits, and the third number gives the number of rows or columns to be used in the plot. The number of rows or columns may be reduced to get the plot to fit on the page. If either the number of rows or columns is specified as zero, then they will set to fill the page maximally. See Analysis Set Command, for a description of the PAGESZ and LINESZ variables which control this.

A rudimentary statistical analysis of the data in the selections is included with the plot.