Building Structures, Modifying and Saving Data

The state of Chimera can be saved to a session file and later restored.

See also: exporting a scene, Write DMS, Write Prmtop

Saving 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. See also: write

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.

Options:

Option when only one model is present: Option when more than one model is present: Option when more than one model is chosen: If one or more of the chosen models contains a trajectory, there will also 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 reflecting the current protein secondary structure assignments are written, along with any other header lines read from PDB input. Even if protein helix/strand assignments have not been changed in Chimera, the output HELIX and SHEET records may differ from the input because helices are written assuming the right-handed α type, and strands are written as if each were a separate sheet.

Saving Mol2 Files

Mol2 format includes atom types and (optionally) partial charges. When a structure is read from a Mol2 file, the atom types and any partial charges are stored as the atom attributes mol2type and charge. The input bond orders are also stored. Unless the user specifies writing Amber/GAFF types instead, output Mol2 files include Sybyl atom types. The Sybyl types read from input will be used, if available; otherwise, Chimera atom types will be translated into Sybyl atom types. As there is not a simple one-to-one relationship between Chimera and Sybyl atom types, users may wish to check the Sybyl type assignments, particularly for nonstandard residues. Similarly, if bond orders were not read from Mol2 input, they will be guessed upon output. Values for the charge attribute can be assigned within Chimera, for example using Add Charge. If no charge values have been read or assigned, the partial charges will be written as zero.

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. See also: write

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.

Option when only one model is present:

Option when more than one model is present: Option when more than one model is chosen: Further options:

Saving Maps after Fitting

Simply saving a map to a file after fitting will not save its new position, because the map file formats do not include rotation information. One way to save the new position is to save a Chimera session, which preserves the translations and orientations of all models. However, if data files are needed for use in another program:

If the goal is to save a map repositioned with translation only (not rotation), the map origin can be changed in the Coordinates section of Volume Viewer or with the volume command (see Dimension and Scale Options) before saving. However, not all programs will use the origin specified in the map file, so it may still be necessary to resample as described above.


UCSF Computer Graphics Laboratory / January 2018