Modifying and Saving Data

The state of Chimera (including data) can be saved to a session file and later restored.

• Atomic coordinate data can be modified by
  • deleting atoms
  • bond rotation
  • amino acid rotamer swapping
  • adding hydrogens, counterions, and solvent
  • structure building and minimization
  • generating multimers with Multiscale Models or Unit Cell
  • simply moving entire models as rigid bodies, such as when superimposing structures or fitting them into maps
  and saved using the command write or the dialogs described below for PDB and Mol2.
  
  
• Volume data can be modified by
  • Volume Viewer (see Coordinates, Region bounds, Subregion selection, and Zone)
  • Volume Eraser
  • Volume Filter
  • the commands volume, mask, and vop
  • keyboard shortcuts for volume editing
  and saved using Volume Viewer (the File menu) or the command volume.
  
  
• Sequence alignments can be edited and saved using Multalign Viewer.

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.

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:

• Save displayed atoms only - only write coordinates of atoms that are displayed
• Save selected atoms only - only write coordinates of atoms that are selected

• Use untransformed coordinates - write coordinates without applying any rotations and translations that have been performed in Chimera

• Save relative to model [model] - save coordinates relative to the untransformed coordinates of a specified reference model (otherwise, transformed coordinates will be saved). 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.

• Save multiple models in
  • a single file - one PDB file containing all chosen models, with MODEL/ENDMDL records delimiting the coordinates of each (technically, this treatment is only correct for models with identical sets of atoms, but may be convenient in the more general case of disparate models)
  • multiple files [appending model number] - a different PDB file for each model, named by appending model ID number (model or model.submodel) to the specified file name, before the ".pdb" suffix, if present

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

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.

Option when only one model is present:

• Use untransformed coordinates - write coordinates without applying any rotations and translations that have been performed in Chimera

• Save relative to model [model] - save coordinates relative to the untransformed coordinates of a specified reference model (otherwise, transformed coordinates will be saved)

• Save multiple models in
  • a single file [individual @MOLECULE sections]
  • multiple files [appending model number] - a different Mol2 file for each model, named by appending model ID number (model or model.submodel) to the specified file name, before the ".mol2" suffix, if present
  • a single file [combined @MOLECULE section] - if the models are all single-residue and the model names are unique but the residue types are not, the model names will be used as substructure names, and the option to include residue numbers in substructure names (below) will be ignored

• Use Sybyl-style hydrogen naming (e.g. HE12 rather than 2HE1) - move leading numerals to the ends of hydrogen names
• Include residue sequence numbers in substructure names - generate substructure names with embedded residue numbers, for example, ALA85 rather than ALA
• Write current selection to @SETS section of file - make the currently selected atoms a SET (as used to specify the rigid portion of a ligand in DOCK)