Using the `Write File' action, you can write the loaded frames to file in either the PDB or the CRD ASCII formats, or you may write to a binary file following the DCD format. This may be used to write out a new trajectory in a single file after assembling many frames from different sources (such as PDB CRD, or DCD files, or even from a remote simulation). You can also use this, in combination with Read File, as a way to make PDB files from a DCD/CRD trajectory.
You can either save the entire stored trajectory, or a slice of the data by using the Amount chooser. Then select the appropriate output file type in the File Type chooser, and press the Write button in the bottom right corner. This brings up the file browser, which you can use to enter the new filename. Once you press the Write button in the browser, the file will be written without further confirmation. See section on atomselect command for information on how to write atom coordinates for an atom selection in a PDB file.