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
Examples: ARU 3555 7564 -1555 ARU 3564.01
ARU
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
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
Include the specified atoms in the atom list. See EXCLUDE.