Building Structures, Modifying and Saving Data

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

• Atomic coordinates can be modified or generated in Chimera in many ways, including
  • bond rotation
  • amino acid mutation and rotamer swapping
  • adding hydrogens
  • deleting atoms
  • structure building
  • Modeller calculations: comparative (homology) modeling, building missing segments, refinement
  • minimization
  • generating multimers (sym, Unit Cell, Multiscale Models)
  • repositioning by superimposing structures or fitting into maps
  • renumbering residues and changing chain IDs
  and saved using the command write or the dialogs described below for PDB and Mol2.
  
  
• Sequence alignments can be generated in Chimera
  • by sequence search and retrieval of hits with Blast Protein (pseudo-multiple)
  • by Match -> Align from the spatial overlap of superimposed structures (multiple)
  • as a by-product of superposition with MatchMaker (pairwise)
  and edited and saved using Multalign Viewer.
  
  
• Volume data (maps) can be modified or generated in Chimera by
  • Volume Viewer (see Coordinates, Region bounds, Subregion selection, and Zone)
  • Volume Eraser
  • Volume Filter
  • molmap to simulate a map from atomic coordinates
  • commands volume, vop, mask
  • keyboard shortcuts for volume editing
  • fitting (but see note on saving after fitting)
  and saved using Volume Viewer (the File menu) or the command volume. Related data:
  • markers/paths can be created and saved with Volume Tracer
  • segmentations can be created and saved with Segger

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:

• 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. In the case of multiple models containing different sets of atoms, the CONECT records should be removed before the file is read back into Chimera, as there is no mechanism for handling the different CONECT records for the different models.
  • multiple files [file name must contain $name or $number] - a different PDB file for each model, named by substituting the model name for $name and/or the model ID number (model or model.submodel) for $number in the specified file name; if this substitution does not produce unique file names, each file will contain only the last appropriate model

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.

• Large-structure serial numbering indicates how to accommodate structures so large that the numbering fields in standard PDB format would overflow (output for smaller structures is not affected):
  • Amber handles atomic models with > 99,999 atoms by “stealing” a column to the left of the atom numbering field in standard PDB format
  • hybrid-36 (default) handles atomic models with > 99,999 atoms (up to 87,440,031) and/or > 9999 residues in a chain (up to 2,436,111) by incorporating alphabetical characters (details...)

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:

• 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 [file name must contain $name or $number] - a different Mol2 file for each model, named by substituting the model name for $name and/or the model ID number (model or model.submodel) for $number in the specified file name; if this substitution does not produce unique file names, each file will contain only the last appropriate model
  • 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 Amber/GAFF atom types instead of Sybyl atom types - include the Amber/GAFF atom types assigned by Add Charge (or command addcharge) instead of Sybyl atom types; if any atom in the chosen models lacks an Amber/GAFF type assignment, file-writing will halt and an error message will be displayed. Mol2 files with Amber/GAFF types are not suitable for reading back into Chimera, as the types are likely to be misinterpreted.
• Write current selection to @SET section of file - make the currently selected atoms a SET (as used to specify the rigid portion of a ligand in DOCK)

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:

• When a map has been fit to an atomic structure, save the PDB file relative to the map rather than vice versa.
• When a map has been fit to another map, a new map can be created in the new orientation by resampling the map that was fit, on the grid of the map to which it was fit. Resampling can be performed with the command vop resample. Resampling uses interpolation and may cause some loss of resolution. The new, resampled map can be saved as described above. (Even if the map was not fit to another map, however, a separate zero-valued map to serve as a grid for resampling can be created with vop new.)