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Trajectory Manager Widget
Leif Laaksonen CSC 2002
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This is the main trajectory control widget. Before you can process a trajectory file you have to import a coordinate file to define the molecule topology and the atom labels because some trajectories contain only atom coordinate information.

Steps to do:

  1. Click of the button for the trajectory type you will analyze or look at. The buttons are on the right.
  2. Select a file from using file browser (Browse button).
  3. Press the "Import file" button to read the trajectory information.
  4. When the file has properly been processes you can reed the number of frames in the file down on the page. There will also be display information about from which frame the display will start and at which frame it will stop and the frame step. Usually you don't have to touch this information att all.
  5. To display the frames as loop starting from the first defined to the last click at the button with a triangle. To stop the display press the button with a square.

The supported trajectory formats are:

AMBER
Unformatted Amber trajectory file. In the utility directory there is program for the conversion of a formatted trajector into a unformatted one. More information can be found from the AMBER Web pages http://www.amber.ucsf.edu/amber/formats.html.
AMBER(F)
Formatted Amber trajectory file. It is recommended that only unformatted trajectories are used. In the utility directory there is program for the conversion of a formatted trajector into a unformatted one. More information can be found from the AMBER Web pages http://www.amber.ucsf.edu/amber/formats.html.
CERIUS2
Unformatted binary CERIUS2 trajectory file.
CHARMM/CHARMm
Unformatted binary CHARMM/CHARMm trajectory file.
DISCOVER
Unformatted binary DISCOVER trajectory file.
GROMOS
Unformatted GROMOS trajectory file.
GROMOS96
Formatted ascii GROMOS96 trajectory file.
HYPERCHEM
Unformatted binary HyperChem trajectory file.
MUMOD
Unformatted binary MUMOD trajectory file. The MUMOD program is developed by Dr. Olle Teleman.
TINKER
Formatted TINKER trajectory file.
XMOL
Formatted ascii XMOL (multiset) trajectory file.
XPLOR
Unformatted binary XPLOR trajectory file.
YASP
Unformatted binary YASP trajectory file. The YASP program is developed by Dr. Florian Muller-Plathe (.

Trajectory display control:

By default the atom connection table is NOT recalculated in between the different frames. However, sometimes it's preferable to recalculate the connection table. This can be done by clicking the "Atom reconnection" to "ON".

The same is true for atom hydrogen bond table except that then "Hbond recalculation" is turned "ON" not all hydrogen bonds are recalculated. Only following connections are recalculated:

For the formatted trajectory files there are two methods available:

It's possible to display the frame number of the current frame. To display the frame number click "Display frame number: on" or off to turn it off.

File browser to select a trajectory file.

Line command: see trajectory command

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LUL/2002
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