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 |
| 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 |