Attributes are properties of atoms, residues, chains, models, and other entities in ChimeraX. Each attribute has a name and a data type: Boolean, integer, floating-point (real), character string, or color. For example, atomic B-factors read from mmCIF or PDB input are assigned as a floating-point atom attribute named bfactor.
Attributes can be:
Attributes are saved in sessions. Selected attributes are listed below. See also: Modeller Results
The table below gives the names of selected attributes along with descriptions of their value types for command-line specification. Although the table only shows = (equal to) right after the names of any non-Boolean attributes, other relationship operators such as != (not equal to) and < (less than) may be used to specify values or value ranges, depending on the type of attribute. Additional attributes can be created (more...).
| ← Selected Atom Attributes (see also info atoms, info atomattr) | |
| alt_loc=ID | ID is the identifier of the alternate location being used for the atom; a single blank space is assigned to atoms without alternate locations; see also num_alt_locs |
| area=sasa | sasa is the solvent-accessible surface area of the atom calculated with measure sasa |
| atomspec=identifier | identifier includes chain ID, residue number, and atom name, for example /A:310@C2 |
| bfactor=bfactor | bfactor is the B-factor value of the atom |
| charge=q | q is the atomic partial charge assigned by running addcharge |
| color=color | color is the color of the atom (assigned on a per-atom basis) |
| display | whether display is enabled at the atom level, see display hierarchy |
| draw_mode=mode | mode is the style of an atom, 0 (sphere), 1 (ball), or 2 (stick) |
| frame=N | for markers on volume series data, the associated time step within the series (N = 0, 1, ...) for synchronized playback |
| gaff_type=gtype | gtype is the GAFF atom type assigned by running addcharge |
| idatm_type=type | type is the atom type |
| name=name | name is the atom name |
| num_alt_locs=N | N is the number of alternate locations of the atom, > 1 for atoms with alternate locations, 0 for those without; see also alt_loc |
| num_bonds=N | N is the total number of atoms bonded to the atom, including those linked by missing-segment pseudobonds |
| num_explicit_bonds=N | N is the total number of atoms bonded to the atom, not including those linked by missing-segment pseudobonds |
| occupancy=occupancy | occupancy is the occupancy value of the atom |
| radius=radius | radius is the current VDW radius of the atom in Å |
| serial_number=N | N is the atom serial number in the input file |
| ← Selected Residue Attributes (see also info residues, info resattr) | |
| amber_name=aname | aname is the AMBER residue name (for standard residues only) assigned by running addcharge |
| area=sasa | sasa is the solvent-accessible surface area of the residue calculated with measure sasa |
| chain_id==ID | ID is the chain identifier of the residue; see also chain attributes |
| is_helix | whether peptide secondary structure type is helix |
| is_strand | whether peptide secondary structure type is strand |
| ss_type=type | peptide secondary structure type: 0 for coil (neither helix nor strand), 1 for helix, 2 for strand |
| ss_id=N | N indexes secondary structure elements from N→C in a protein chain: 1 for residues in the first helix and first strand, 2 for those in the second helix and second strand, and so on; 0 for residues not in protein helix or strand |
| name=xyz | xyz is the residue name (not case-sensitive, but all-numeric names should be enclosed in quotation marks) |
| num_atoms=N | N is the total number of atoms in the residue |
| number=N | N is the residue number |
| omega=angle | angle is the peptide backbone ω dihedral angle (CA(i-1)-C(i-1)-N-CA) |
| phi=angle | angle is the peptide backbone φ dihedral angle (C(i-1)-N-CA-C) |
| psi=angle | angle is the peptide backbone ψ dihedral angle (N-CA-C-N(i+1)) |
| chiN=angle | angle is the Nth χ dihedral angle of an amino acid sidechain, where N=1 refers to the torsion angle around the Cα-Cβ bond, N=2 refers to that around the Cβ-Cγ bond, etc. |
| sym_chiN=angle | angle is the smaller of the equivalent measurements for the Nth χ dihedral angle of an amino acid sidechain when there are chemically identical substituents (e.g., two carboxylate oxygens) in symmetric positions |
| polymer_type=type | type is 0 for nonpolymer, 1 for protein, 2 for nucleic acid; see also chain attributes |
| ribbon_color=ribcolor | ribcolor is the color of the residue's ribbon segment (however, this can be assigned even when the residue is a type that does not have any ribbon, such as water) |
| ribbon_display | whether ribbon display is turned on for the residue (however, this can be true even when the residue is a type that does not have any ribbon, such as water) |
| seq_conservation=cons | cons is the Conservation header value in the Sequence Viewer for the column associated with the residue; the alignment must contain at least two sequences |
| seq_identity=identity | identity is the percentage of a column in the Sequence Viewer that contains the most common nongap character in that column; it does not depend on the type of the associated residue |
| seq_rmsd=rmsd | rmsd is the RMSD header value in the Sequence Viewer for the column associated with the residue; the attribute exists only when at least two structure chains from different models are associated with the alignment and the RMSD header is shown |
| worm_radius=wrad | wrad is the radius of a biopolymer residue in a worm representation previously generated with Render by Attribute or the cartoon byattribute (worm) command |
| asym_detail=value | the value for a chain in IHM data is read from the mmCIF field “struct_asym.details” |
| entity_name=name | the name for a chain (entity) in IHM data is read from the field “ihm_struct_assembly.entity_description” and reported in the Log |
| ← Selected Chain Attributes (see also info chains, model information) | |
| chain_id==ID | ID is the chain identifier of the polymer (whereas the residue attribute chain_id also applies to nonpolymeric residues) |
| characters=sequence | sequence is the entire sequence of the polymer chain, in one-letter residue codes |
| polymer_type=type | type is 1 for protein, 2 for nucleic acid |
| identity=="atom-spec" | the atom-spec is any atom specification string (surrounding quotation marks required) and will be taken to indicate the biopolymer chains containing those atoms. The attribute means that a chain has the same sequence as any of the specified chains. For example, //identity=="#1/A,B" would specify all chains with sequences the same as either chain A or chain B in model 1. Chain sequences are determined from PDB SEQRES records or the mmCIF equivalent, if available, otherwise from the atomic coordinates. See also color byidentity and the sequence option of select. |
| ← Selected Atomic-Model Attributes (see also info models, model information) | |
| autochain | whether “chain trace” pseudobonds should be added between consecutively bonded residues when the covalent bonds are hidden (e.g., when α-carbons are the only backbone atoms shown) |
| ball_scale=factor | factor is ball radius relative to VDW radius, see size |
| color=color | color is the color assigned on a per-model basis |
| display | whether display is enabled at the model level, see display hierarchy |
| name=name | name is the name of the model |
| num_atoms=N | N is the total number of atoms in the model |
| num_residues=M | M is the total number of residues in the model |
| res_numbering=scheme | scheme can be author (initial default), canonical, or uniprot; available for biopolymer structures with the relevant metadata, typically from the wwPDB |
| selected | whether any atom(s) and/or bond(s) within the model are selected |