Worms

Worms are specialized cartoons in which “fatness” reflects the values of an attribute such as bfactor or seq_conservation. In the example image, the average atomic B-factor per amino acid residue is shown with both coloring and worms. The structure is a trimer of E. coli porin (PDB 1pho). For image setup, see the command file worms.cxc.

Worms are available in ChimeraX v1.8 daily builds 3/12/24 and newer. Worms and coloring by attribute can be done with the Render by Attribute tool or commands cartoon byattribute (aka worm) and color byattribute.

B-factor Coloring

Atomic B-factor values are read from PDB and mmCIF input files and assigned as attributes that can be shown with coloring and used in atom specification. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB 4hvp). For complete image setup, including positioning, color key, and label, see the command file bfactor.cxc.

Additional color key examples can be found in tutorials: Coloring by Electrostatic Potential, Coloring by Sequence Conservation

More images...