Write saves the atomic coordinates of the specified molecule model in a file named filename of the specified format. The model_number is optionally preceded by #. If filename is omitted, a dialog for specifying the name and location will appear. To save multiple models at once, use the Save PDB or Save Mol2 dialog instead.
Only atomic coordinates are saved, not atomic display status, color, or radius. Non-molecule models (surfaces, VRML models, etc.) are not saved.
See also: getcrd, pdbrun, save, export, writesel, Write DMS, Write Prmtop, saving data
format pdb | mol2
Which output file format to generate: PDB or Mol2. Files saved in pdb format (default) include HELIX and SHEET records reflecting the current protein secondary structure assignments, as well as 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.
Write only the coordinates of selected atoms.
Write only the coordinates of displayed atoms.
Write coordinates relative to the untransformed coordinates of model number n. Otherwise, the coordinates will be written as currently transformed. The model number is optionally preceded by #. The relative option 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 the model contains a trajectory, write all frames that have been read in with MD Movie. Otherwise, only the current frame will be written out.
serialNumbering amber | h36
If writing pdb format, 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
- h36 (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...)
If writing mol2 format, generate substructure names that include residue numbers (for example, ALA85 rather than ALA).
atomTypes amber | gaff | sybyl
For mol2 format, setting atomTypes (or atomtypes) to amber or gaff indicates that the output file should include Amber/GAFF atom types instead of Sybyl atom types. Amber/GAFF atom types are assigned by Add Charge or the command addcharge. If any atom being written 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. **