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Attributes

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

Attribute Names

Selected attribute names are listed below. Additional attributes can be created (more...).

Selected Atom Attributes (see also info atomattr)
alt_loc=ID ID is the identifier of the “dominant” alternate location, i.e., which set of coordinate, occupancy, and bfactor values are being used for the atom; see also num_alt_locs
area=sasa sasa is the solvent-accessible surface area of the atom calculated with measure sasa
bfactor=bfactor bfactor is the B-factor value of the atom
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
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 the atom has
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 resattr)
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
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 Conservation header value in the Sequence Viewer for the column associated with the residue; the alignment must contain at least two sequences
seq_rmsd 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
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
chain_id=ID ID is the chain identifier of the polymer (whereas the residue attribute chain_id also applies to nonpolymeric residues)
polymer_type=type type is 1 for protein, 2 for nucleic acid

Selected Atomic-Model Attributes
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

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2020