Saving Coordinates

PDB Files

The dialog for saving PDB files can be invoked with File... Save PDB or Actions... Write PDB in the Chimera menu, the Write PDB... button on the Selection Inspector, 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.

Further options:

If multiple models are chosen, they can be saved as a single PDB file (separated by END records) or as 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 whose coordinate sets have been read in with MD Movie. A model will not be recognized as a trajectory until more than one set of coordinates has been read.

Besides atomic coordinates, HELIX and SHEET records (see the Intro to PDB Format (PDF)) are written out. These reflect the current residue helix/strand assignments. However, helices are assumed to be of the right-handed alpha type, and information on strands is written as if each were a separate sheet (information on the actual number of sheets and strand register is not included).

See also the command write.

Mol2 Files

The dialog for saving Mol2 files can be invoked with File... Save Mol2 in the Chimera menu. 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.

Further options:

If multiple models are chosen, they can be saved as a single Mol2 file (in either a single @MOLECULE section or separate @MOLECULE sections) or as multiple Mol2 files. Multiple Mol2 files are named by appending model ID number (model or model.submodel) to the specified file name, before the ".mol2" suffix, if present.

Mol2 files include columns for atom types and partial charges. Mol2 files written from Chimera contain Sybyl atom types translated from the atom types in Chimera; partial charges are set to zero, unless atoms have been assigned values for the attribute named charge (for example, by using Dock Prep). As there is not a simple one-to-one relationship between the atom types, users may wish to check the Sybyl type assignments, particularly for nonstandard residues.


UCSF Computer Graphics Laboratory / January 2006