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.
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 |
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 |
num_atoms=N | N is the total number of atoms in the residue |
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 |
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) |
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) |
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 |
← 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 |