This form is used to add, save, or delete coordinates sets (also referred to here as frames) from a molecule. Usually these coordinates come from successive frames of a trajectory but, as shown in the tutorial A Quick Animation, can also be distinct conformations of the same structure.
When this form is used, it will affect only the molecule selected in the Selected Molecule chooser. There are three types of actions which can take place; read frames from or write frames to a file (in the CRD, DCD or PDB format) or delete frames from the current animation.
VMD can read in new coordinate sets from PDB files (to add a single new frame to the animation), from ascii CRD files (which may contain several frames), from binary DCD files (which may also contain several frames), or from Gromacs trajectory files. The new coordinate sets are appended to the end of the stored animation list for the selected molecule. At present, there is no way to use Babel to append non-natively-supported files. The format is determined by selecting the appropriate name in the File Type chooser. If you want to read in all the information from the file, make sure that the Amount chooser says `All', then press the Read button in the bottom right corner. This will bring up the file browser so you can select the file. (Unlike the Files form, the file is loaded immediately after the filename is entered in the file browser.)
Sometimes you may not want to read in a whole CRD/DCD file. For example, you may only want the last frame, or every tenth frame. You can do this by choosing the `Selected' option in the Amount chooser. This brings up the frame skip selection controls. Once you've chosen the appropriate values, press the Read button to bring up the file browser and finish as mentioned in the previous paragraph. The Amount options are ignored when reading in PDB files.
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, DCD or Gromacs 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.
This provides a way to delete frames from memory. First, choose the frames you wish to delete with the Amount chooser and (possibly) the frame skip controls, then press the Delete button. There is no confirmation of deletions.
One problem with this mechanism is there is no way to delete every frame except for those given by the frame skip. You can get around this by writing the skip selection to a CRD/DCD file, deleting all the frames from memory, then reading the skip back in from disk.
The meaning of this option varies depending on the action. If `All' is selected, then all the frames will be read from the file, or all the frames will be written to the file, or all the frames will be deleted from memory.
The other option is `Selected.' This will bring up three controls, labeled Begin, End, and Skip. These make it possible to use a subset of the frames, starting at frame Begin and selecting every Skip frames until the End is reached. For instance, to select every fifth frame between frames 14 and 98, set:
(Remember that frame numbers in VMD start at 0, so frame 0 is the first frame.) The value `-1' is a special number; setting Begin to -1 is the same as starting at the first frame, End = -1 is the same as ending at the last frame, and Skip = -1 is the same as taking one step.
When the Action is `Read File', the selection is applied to the frames from the file to be read. When it is `Write File', the selection determines the frames to be written, and when `Delete Frames', the selection determines the frames to be deleted from memory.
