Chimera Commands Index

write options model_number [ filename ]

Write saves the atomic coordinates of the specified molecule model in a file named filename of the specified format. The model_number should not be 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.


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.
relative n
Write coordinates relative to the untransformed coordinates of model n; otherwise, the coordinates will be written as currently transformed. 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.
If writing mol2 format, generate substructure names that do not include residue numbers (for example, ALA rather than ALA85).

See also: getcrd, pdbrun, save, export, writesel, Write DMS, Write Prmtop, saving data