Each file of coordinates opened in Chimera becomes a model with an associated model number. Some PDB files are further subdivided into multiple structures designated with MODEL and ENDMDL records; thus, the concept of submodels was created to allow unique atom specifications even when multiple MODELs contain identical residue and atom names.
Molecular surfaces and VRML objects are also assigned model numbers. Objects, surfaces, and molecules can share a number.
The command modeldisplay sets the display status of entire models and submodels. If the atom-spec is blank, all open molecule models will be affected; otherwise, the entire model(s) containing atom-spec will be affected. In contrast, display controls display at the level of individual atoms and bonds, and surface controls display at the level of individual atom surfaces. VRML objects can only be completely displayed and undisplayed, with modeldisplay, objdisplay or the Model Panel show and hide functions.
~Modeldisplay does not reset the display status of individual atoms, bonds, and atom surfaces, but overrides them (see display hierarchy). This is convenient for temporarily hiding a molecule from display without disrupting its display setup, which may have been rather elaborate. For example, it is common to display the backbone of a protein plus only the side chains of interest and a few important crystallographic waters. Attaining this state may take several commands or menu actions. ~Modeldisplay/modeldisplay can then be used to hide and reveal the entire protein without disrupting this display setup.
Example:
~modeldisp #0.1-5- undisplay submodels 1 to 5 of model 0
~modeldisp #1- undisplay model 1 as a whole
See also: display, objdisplay, open, surface, the Model Panel