________
_A0=four atoms defining a torsion angle
 A1=physical atoms in system of molecules
 A2=bond lengths in system of molecules
 A3=bond angles in system of molecules
 A4=torsion angles in system of molecules
 A5=physical atoms in system of molecules
#A6=
#A7=
 A8=subset of physical atoms
#A9=
________
 B0=atoms in residue base groups [forward order]
 B1=atoms in chain base groups [forward order]
 B2=atoms in torsion-contracted chain base groups [forward order]
 B3=atoms in atom-contracted chain base groups [forward order]
 B4=patches on bod
 B5=atom pairs within 1 probe diameter supporting torus
 B6=base resudues used in deformation screen
 B7=element impulses
_B8=bins of interval [0.00,1.00]
 B9=compositions
________
 C0=atom pairs with distance constraint in system of molecules
 C1=atom pairs with distance constraint with 2nd atom in order of generation
 C2=side chain rotamers
 C3=atom pairs with distance constraint used in exact segment deformation
 C4=(psi,omg,phi) conformations
 C5=atom triples supporting probe fixed position
 C6=(del,eps,zet,alp,bet,gam,del) conformations
 C7=ss states {#,H,E,C}
 C8=dock configs
 C9=full charges
________
 D0=search subspace deformations
 D1=segment backbone deformations
 D2=combined backbone deformations
 D3=side chain conformations
#D4=
 D5=low density surface element
#D6=
#D7=
 D8=high SCORE sheet configs
 D9=high SCORE pack configs
________
 E0=sub-block pairs with interaction energy
 E1=sub-block pairs with interaction energy following contraction
 E2=atom pair within small distance of repulsion overlap
_E3=atom pairs overlapping in overlap removal
 E4=pairs of H-bonds in extendable patterns
 E5=concave edges
 E6=convex edges
 E7=residue impulses
 E8=atom pairs (chg-chg), (chg-hp), (hp-chg) with torsion dependence
 E9=atom pairs (don-acc), (acc-don) with torsion dependence
________
 F0=atoms in residues [backward order]
 F1=atoms in chains [backward order]
 F2=atoms in atom-contracted chain [backward order]
#F3=
 F4=collections of consistent fragment alignments
 F5=concave faces
 F6=saddle faces
 F7=convex faces
#F8=
#F9=
________
 G0=atoms in residue forward groups [forward order]
 G1=atoms in chain forward groups [forward order]
 G2=atoms in torsion-contracted chain forward groups [forward order]
 G3=atoms in atom-contracted chain forward groups [forward order]
 G4=subsets of C4 (psi,omg,phi) conformations
 G5=grid points for dot surfaces
 G6=generated residues used in deformation screen
 G7=elements in chain
#G8=
 G9=bods in pack
________
 H0=atoms in residue backward groups of branch torsions [branch backward order]
 H1=atoms in chain backward groups of branch torsions [branch backward order]
 H2=atoms in chain backward groups of branch torsions [branch backward order]
_H3=hydrogen bonds
_H4=10 degree intervals in partition of torsion angles values [-190, 190)
 H5=circles
 H6=pH values of titration
_H7=displacements
 H8=hash of 0,1,2, or 3-bod pattern
 H9=peptide plane H
________
_I0=regions of protein backbone conformation space
_I1=defect energy levels attributed to torsion angle values
 I2=pdb record at site of defect
_I3=conformations within a characteristic distance
 I4=insertions or deletions
 I5=atoms within probe diameter of central atom
 I6=alt name for Y8
 I7=high SCORE chain states
 I8=ionization states previously encountered
 I9=alt name for Y9
________
 J0=pairs of adjacent torsion angles in residues
 J1=pairs of adjacent torsion angles in chains
 J2=pairs of adjacent torsion angles in torsion-contracted chains
 J3=residue shifts in deformation
 J4=residues of hydrophob patch
 J5=string of CYS torsions [forward order] modified for crosslinking
_J6=residues of a packing unit in homology model building
 J7=block of impulses consistent with pattern
#J8=
#J9=
________
 K0=cross links for ring closure in residues
 K1=subsets of degrees of freedom in regularization
_K2=patterns of subsets of degrees of freedom in residues
_K3=profiles [non-proline and proline] of defect energy attributed to omega values
 K4=elements of bod
 K5=string of CYS torsions [backward order] modified for crosslinking
 K6=cycle of edges bounding a fragment of surface
 K7=high SCORE chain states
 K8=ionization states with lowest dg
#K9=
________
 L0=residues in dataset
 L1=20 naturally occurring amino acids
_L2=lines
 L3=peptide residues in ising model dataset
 L4=nucleotide residues in ising model dataset
 L5=physical atoms of CYS modified for crosslinking
 L6=edge bounding a fragment of surface on a sphere or torus
#L7=
#L8=
#L9=
________
 M0=systems of molecules of a trajectory
 M1=systems of molecules of a family
 M2=minimization steps
 M3=subsets of degrees of freedom in local minimization
 M4=minimization macro steps
#M5=
#M6=
_M7=subset of high SCORE chain states
 M8=subset of strands isolated from complement
 M9=subset of bods isolated from complement
________
#N0=
_N1={0,1}
_N2={1,2}
_N3={1,2,3}
_N4={1,2,3,4}
#N5=
_N6={1,2,3,4,5,6}
#N7=
#N8=
#N9=
________
_O0=side chain torsions in residues [iupac order]
 O1=twists of hydrophob patches
 O2=torsion of intervening strings for atom pairs E2
#O3=
 O4=occurances of atom type used in distance constraints
_O5=non-equivalent topologies of forward groups
#O6=
_O7=clusters of naturally occurring amino acid types
 O8=torsion of intervening strings for atom pairs E8
 O9=torsion of intervening strings for atom pairs E9
________
 P0=physical atoms in residues [iupac order]
 P1=physical atoms in chains [iupac order]
 P2=physical atoms in blocked residues [iupac order]
 P3=patterns of hydrophob patches
 P4=sequence displacements in structure-structure alignment
#P5=
 P6=incomplete side chain heavy atoms variable in homology model building
_P7=clusters of naturally occurring amino acid types
 P8=positions in alignment
#P9=
________
 Q0=torsions in residues [forward order]
 Q1=torsions in chains [forward order]
 Q2=torsions in torsion-contracted chains [forward order]
 Q3=collections of groups [forward or base] forming sub-residue fragments
 Q4=fragment alignments in structure-structure alignment
 Q5=clusters of dots representing connected surfaces
_Q6=side chain torsions variable in rotamers [forward order]
#Q7=
 Q8=backup of config search for sheet/ SCOP domain definition
 Q9=backup of congig search for pack
________
 R0=residues in chains
 R1=residues of search subspace containing variable torsions
#R2=
 R3=residue ranges combined to form sequence space
 R4=res strings containing hydrophob patch
 R5=subset of residues capable of metal binding
 R6=residues with variable side chains in homology model building
_R7=element lengths in residues
#R8=
#R9=
________
 S0=disulfide bonds in system of molecules
 S1=disulfide bonds in torsion contracted system of molecules
_S2=atom types for disulfide bond crosslinking
 S3=atom pair types for disulfide bond crosslinking
_S4=sectors of a circle
#S5=
#S6=
#S7=
 S8=extended strands
 S9=bods
________
 T0=torsions in residues [iupac order]
 T1=torsions in chains [iupac order]
 T2=atom types
#T3=
 T4=atom types used in distance constraints
 T5=torsions in search subspace [iupac order]
#T6=
 T7=element types
 T8=factor subconfigs for sheet alignments
 T9=factor subconfigs for for packings
________
 U0=side chain torsions in residues [branch backward order]
 U1=side chain torsions in chains [branch backward order]
 U2=minimization degrees of freedom
_U3=parameter degrees of freedom
#U4=
 U5=structurally conserved regions
#U6=
 U7=element (type,length) pairs
 U8=all subsystems containing oU strands
 U9=all subsystems containing oU bods
________
 V0=ionizable groups in system of molecules
_V1=discrete confs of peptide planes for N-terminal block
_V2=discrete confs of peptide planes for C-terminal block
#V3=
#V4=
 V5=vertices
 V6=side chain rotamers consistent with substitution
_V7=clusters of element types
 V8=sheets of optimal union of subconfigs
 V9=nonoplar side chain clusters
________
_W0=weights for distance constraints
#W1=
#W2=
#W3=
 W4=hydrophob patches
#W5=
 W6=packing units for side chain placement in homology model building
_W7=clusters of element types
#W8=
#W9=
________
 X0=torsions in residues [backward order]
 X1=torsions in chains [backward order]
 X2=collections of groups [backward] forming sub-residue fragments
_X3=discrete values of confs of the ends of a segment to be deformed
_X4=backbone conformations from dead end elimination on combinatorial space
 X5=concave edges on a torus
 X6=cycles bounding a convex face
 X7=ising model confs per residue
 X8=residues in template chain
#X9=
________
 Y0=triples of adjacent torsion angles in residues
 Y1=triples of adjacent torsion angles in chains
 Y2=triples of adjacent torsion angles in torsion-contracted chains
 Y3=side chains in a packing unit
 Y4=pairs of atom types used in distance constraints
#Y5=
 Y6=cycles on an atom
_Y7=conformations of nucleic acid residues
 Y8=oU-strand subsystems
 Y9=oU-bod subsystems
________
 Z0=chains in system of molecules
_Z1=segments of chains forming SCOP40 domain
 Z2=segments deformed in a step of global minimization
#Z3=
 Z4=consistent fragment alignments
 Z5=convex edges on an atom
 Z6=convex edges in a cycle
#Z7=
 Z8=strands of subsystem
 Z9=bods of subsystem
