Load and visualize a xyz trajectory frame by frame



  • Hi,

    How to load a trajectory (in a single xyz file), and visualize it frame by frame?

    Thanks,

    Luis



  • Dear @luis ,

    To load an XYZ file with a trajectory it needs to be in a special format. For example, a trajectory of 3 hydrogens:

    3
     STEP:           1
     H      0.967485      6.687080      5.821420
     H      2.507099      7.320300      6.535832
     H      2.819131      8.163311      3.557150
     3
     STEP:         2
     H      0.987382      6.755653      5.887846
     H      2.528730      7.288068      6.545012
     H      2.899837      8.187620      3.675997
     
    

    The first number is the number of atoms, the following comment line should contain the word 'Step' (or 'step' or 'STEP'), and the atoms in each step should be in the same order.



  • Once loaded, you should see a Path node in the Document view. You can double-click on it to start/stop the trajectory.

    To play the trajectory frame-by-frame or go to a specific frame, you can use the Inspector - right-click on the Path node in the document and click on "Inspect" - this should open the Inspector for this node. Please note, that some functionality of the Inspector is disabled in the Starter plan version, you can try the Standard or Professional plans for a free 30-day trial period.

    If you don't have access to the Inspector, then you can create Conformations out of the Path. For that, right-click on the Path in the document and click on "Create conformations from paths" - this will create conformations in the document for each frame of the Path. Then you can simply double-click on a conformation in the document to restore it.



  • Great. Thanks @DmitriyMarin


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