PLUTON Manual

The inclusion/exclusion of atoms

ARU (aru1 (aru2 ..)

This instruction adds in a cumulative fashion asymmetric residue units (aru's) to the list of aru's to be drawn. It allows the user to have direct control over the list of residues to be drawn. This instruction is needed only when the automatic maintenance of this list with the JOIN RADII and/or PACK instructions is found to be not adequate. The ARU list may be inspected with the LIST ARU instruction. ARU's (e.g. aru1) are designated by a composite number (ARU) that may be split up into five parts:

        ARU = S*1000 + TX*100 + TY*10 + TZ + 555 + R*0.01

where S is the serial number of the symmetry operator (from the complete list to be inspected with a LIST SYMM instruction) to be applied to the input list of coordinates; TX, TY, TZ are the unit cell translations and R is the residue number. A negative sign of ARU means that the specified residue should not be drawn in the following plots, and may be used to eliminate residues temporarily from the list of residues to be plotted. This may useful in conjunction with the pack instruction. Often residue numbers are not explicitly indicated and the fractional part of ARU effectively set to zero. In this form the complete asymmetric structure unit (ASU) is meant.

        Examples:
        ARU 3555 7564 -1555
        ARU 3564.01

Note: for packing reasons, the number of residues that can be coded is restricted to 9 with corresponding change in aru coding.

ARU NONE/UNIQUE/INTER/RESTORE

The effective ARU list is emptied with the NONE sub-keyword. (A LIST ARU will show that all ARU's now have negative values). The list is reset to what it was after a previous JOIN RADII UNIQUE or INTER instruction with the UNIQUE or INTER keywords respectively. A RESTORE sub-keyword resets all negative entries in the molecule list to their absolute value, so that they are active again. If the effective ARU list is empty when the PLOT instruction is read, a ARU 1555 instruction will be executed automatically.

        Example:
        ARU NONE

EXCLUDE atom-names/atom-types/ALL/NONE/ORIG/UNIQUE/INTER

Exclude the specified atoms from the atom list. ORIG means all the atoms originally input; UNIQUE means atoms generated by JOIN RADII UNIQUE; INTER means atoms generated by JOIN RADII INTER. Bonds are only drawn between included atoms, except that bonds to UNIQUE and INTER atoms are drawn even if these atoms are omitted. Usually, generated atoms need not be specifically included because they duplicate original atoms in generated molecules. The effect of successive INCLUDE and EXCLUDE instructions is cumulative. INCLUDE ALL and EXCLUDE NONE are synonymous; so are INCLUDE NONE and EXCLUDE ALL. The default is INCLUDE ALL.

        Example:
        EXCLUDE H

INCLUDE atom-names/atom-types/ALL/NONE/ORIG/*/&

Include the specified atoms in the atom list. See EXCLUDE.