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Atoms belonging to the backbone as defined in the macromol dictionary.
Bonds belonging to the backbone as defined in the macromol dictionary.
{BIOPOLYMER(option1,option2,...)}
Substructures in a biopolymer. Options are:
- PROTEIN--Selects amino acids in protein chains (including modified amino acids). It is similar to {SEQUENCE(*)}
- DNA--Selects nucleic acids in DNA chains.
- RNA--Selects nucleic acids in RNA chains.
- COFACTOR--Selects cofactor substructures, as defined in the biopolymer dictionaries.
- WATER--Selects water substructures, as defined in the biopolymer dictionaries.
- LIGAND--Selects substructures not included in the above categories and not a carbohydrate, as defined in the biopolymer dictionaries.
Atoms in one group having van der Waals contacts with atoms of the other group. van der Waals parameters stored in the file $TA_ASCTABLES/ATOM_DEF are used.
Use TAILOR SET GENERAL BUMPS_CONTACT_DISTANCE to define the cutoff distance. Negative values allow overlap of van der Waals spheres, positive values prohibit it. Default is 0.0 Å.
Atoms of the specified chirality or pro-chirality. Specify the atoms to search as an expression. Chirality is indicated by the second argument as: R, S, RS, PRO_R, PRO_S, or PRO_RS. If RS or PRO_RS is entered, all centers are included in the set. The default is to search all atoms (*) for all chiral centers (RS).
{FINDCONF(state1+state2+,sequence)}
Monomers having the specified conformational state(s) as defined in the macromol dictionary. Entering a sequence limits the search to the specified regions of the biopolymer ("*" searches whole biopolymer). Separate conformational states by plus signs.
Atoms of the specified type participating in hydrogen bonds. Valid types include: ALL, DONOR, ACCEPTOR, or HYDROGEN. Definitions for the donor and acceptor atoms are in the parameter table $TA_ASCTABLES/ATOM_DEF as H_ACCEPTOR and H_DONOR fields.
Atoms with a metallic ordinal number (according to the periodic table). This set also includes metal atoms in cofactors.
{MONPROP(keyword,minimum,maximum)}
Monomers having the specified property as identified by a keyword and (optional) minimum and maximum values. Enter only the keyword to select all monomers having that keyword. Enter the keyword and a minimum to select monomers with the keyword whose value matches the minimum. The keyword may be any arbitrary string. Values may be real, integer, or string. Properties are stored in the macromol dictionary (molecular weight is stored as MOL_WT).
Monomers of the specified type(s). Types are defined in the macromol dictionary. As many types as desired may be specified as arguments. An asterisk (*) specifies all substructures that are monomers.
{POSSIBLE_HBOND(atom_expression,type)}
Atoms of the specified type which can potentially participate in hydrogen bonds. Valid types include:
Specified atoms which are included in rings of the specified type. Types include:
- I--Internal rings (completely contained within a substructure).
- E--External rings (crossing substructure boundaries).
- EI (IE)--Either internal or external.
Specified bonds which are included in rings of the specified type. Types include:
- I--Internal rings (completely contained within a substructure)
- E--External rings (crossing substructure boundaries)
- EI (IE)--Either internal or external.
{RINGS(substructure_expression,type)}
Substructures in the expression, which are included in rings of the specified type.
{SEQUENCE(sequence1,sequence2,)}
Atoms in monomers of the specified sequence(s). Monomers are defined in the macromol dictionary. See Monomer Sequence Specification for information on how to select specific monomer sequences.
COLOR ATOM {SEQUENCE(GLY=PRO,GLY=GLY)} BLUE
{SEQUENCE(sequence1,sequence2,)}
Bonds in monomers of the specified sequence(s). Monomers are defined in the macromol dictionary.
{SEQUENCE(sequence1,sequence2,)}
Monomers in the specified sequence(s). Monomers are defined in the macromol dictionary.
Atoms belonging to sidechains as defined in the macromol dictionary.
Bonds belonging to sidechains as defined in the macromol dictionary.
{SPHERE(atom_expression,radius)}
Atoms falling within sphere(s) of the specified radius. The expression defines the sphere center(s). When multiple atoms are selected, the final set is the union of sets of atoms within spheres of indicated radius about each center. All spheres have the same radius.
{SPHERE(atom_expression,radius)}
Bonds falling within sphere(s) of the specified radius. The expression defines the sphere center(s). When multiple atoms are selected, the final set is the union of sets of bonds within spheres of indicated radius about each center. Note: Only bonds with both endpoint atoms in the sphere are accepted. All spheres have the same radius.
{SPHERE(atom_expression,radius)}
Substructures falling within sphere(s) of the specified radius. The expression defines the sphere center(s). When multiple atoms are selected, the final set is the union of sets of substructures within spheres of indicated radius about each center. Note: Substructure is accepted, even if only one of its atoms falls within the sphere. All spheres have the same radius.
{SUBST_SPHERE(atom_expression,radius)}
Atoms, bonds, or substructures falling within sphere(s) of the specified radius. The expression defines the sphere center(s). When multiple atoms are selected, the final SUBST_SPHERE set is the union of sets of substructures included in spheres of indicated radius about each center. Note: Substructure is accepted, even if only one of its atoms falls within the sphere (identical to sphere for substructures).
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