The dialog for saving PDB files can be invoked with File... Save PDB in the Chimera menu or write PDB in the Model Panel. The dialog resembles other open/save dialogs, but has additional specific options.
Individual models or blocks of models can be chosen from the Save models list with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block. Only molecule models are listed.
By default, transformed coordinates are saved. However, coordinates relative to the untransformed coordinates of any model can be saved by checking the box marked Save relative to model and choosing the desired reference model from the adjacent pulldown menu. This is useful for preserving the spatial relationship between models. For example, if model 1 has been matched or docked to model 0, saving 1 relative to 0 results in the models being matched or docked in the same way when the model 0 file (original) and the model 1 file (saved relative to 0) are reopened.
If multiple models are chosen, it is possible to save them to a single PDB file (separated by END records) or to multiple PDB files. Multiple PDB files are named by appending model ID number (model or model.submodel) to the specified file name, before the ".pdb" suffix, if present.
If one or more of the chosen models contains a trajectory, there will be an option to Save the current frame or all frames. In this context, "all frames" means all frames that have been viewed with Movie. A model will not be recognized as a trajectory until more than one frame has been viewed.
See also the command write.