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Frame snapshot

The Frame snapshot option allows the extraction of one or several frames in PDB format from a MMTK NetCDF trajectory. Clicking on it, the dialog shown in figure 4.12 will pop up.

Figure 4.12: The dialog used to export trajectory frames to a PDB file.

To perform the frame extraction, the following input fields must be filled:

- NetCDF input file
  Format: string
  Default: None
  Description: a MMTK NetCDF trajectory file of the system must be provided for the extraction. If a trajectory is currently loaded, it will be proposed by default for the frame extraction.

- Selected frames
  Format: integer or Python expression or string
  Default: 1
  Description: this field will store the frames selected for extraction. The format for the Selected frames field can be:
  - an integer specifying the index of a single frame to extract
  - a valid Python expression that will generate a list of integers where each integer specify the index of a frame to extract.
  - a string with the following format:
    min 1:max 1:skip 1 sep ... sep min N:max N:skip N
    where sep can be a white space, a comma or a semicolon and each block min i:max i:skip i will specify a range of frames including frame min i to frame max i by jump of skip i frames.

- PDB output file
  Format: string
  Default: None
  Description: this field will store the name of the PDB output file that will contain the extracted frames. The line
  REMARK Frame i
  will be written before each written frame i.

Next: Convert NetCDF to ASCII Up: The File menu Previous: VASP to MMTK Contents