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Attributes

Attributes are properties of atoms, residues, 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.

Attribute Names

See also: info bondattr

Selected Atom Attributes (see also info atomattr)
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)
idatm_type=type type is the atom type
name=name name is the atom name
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
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
phi=angle angle is the peptide backbone φ dihedral angle (Ci-1-N-CA-C)
psi=angle angle is the peptide backbone ψ dihedral angle (N-CA-C-Ni+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
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)
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 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 / April 2019