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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

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 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
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 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 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
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 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
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
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 / August 2021