Chimera Commands Index

Usage:
write [ selected ] [ displayed ] [ relative n ] [ trajectory ] model_number [ filename ]

Write saves the coordinates of the specified molecule model as a PDB file named filename. The model_number should not be preceded by #. If filename is omitted, a dialog for specifying the name and location will appear. Only atomic coordinates are saved; atomic display status, color, and radius are not included. The write command does not work for non-molecule models (surfaces, VRML models, etc.). To save multiple models at once, use the Save PDB Dialog instead.

The selected option specifies that only coordinates of selected atoms should be written. The displayed option specifies that only coordinates of displayed atoms should be written.

The relative option specifies that the coordinates written out should be 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.

The trajectory option specifies that if the model contains a trajectory, all frames should be written out. In this context, "all frames" means all frames whose coordinate sets have been read in with MD Movie. Otherwise, only the current frame will be written out.

Besides atomic coordinates, HELIX and SHEET records (see the Intro to PDB Format (PDF)) are written out. These reflect the current residue helix/strand assignments. However, helices are assumed to be of the right-handed alpha type, and information on strands is written as if each were a separate sheet (information on the actual number of sheets and strand register is not included).

See also: getcrd, pdbrun, save, writesel, Saving Coordinates