Molecule Tutorials - Herong's Tutorial Examples - 1.01, by Dr. Herong Yang
What Is State in PyMol
This section provides a quick introduction about 'state', which represents a particular arangement of molecule structure objects in PyMol.
What Is State in PyMol? A state is a concept used by PyMol to represent a particular arangement of molecule structure objects.
PyMol allows you to create multiple states, which can be used to build frames to create a movie.
When you start PyMol, it has no frames and no structure objects.
When you load the first molecule structure from a file using the "load file_name" command, PyMol creates the first state #1, and adds the structure as a new object to state #1. The new object is named with the file name.
If you load the second molecule structure from another file using the "load file_name" command, PyMol adds the second structure as a new object to state #1. The new object is named with the file name.
If you want to create state #2 and load the second structure to state #2, you need to specify the state # in the load command as:
load file_name, object_name, state
Here is a PyMol command script that creates 3 states with 3 objects from 3 files.
# Create-Multiple-States-from-Files.pml # delete exsiting objects and frames delete all # create state 1 with methane molecule as the object load Molecule-Methane.sdf, Methane, 1 # create state 2 with alcohol molecule as the object load Molecule-Alcohol.sdf, Alcohol, 2 # create state 3 with benzene ring as the object load Benzene-Ring.sdf, Benzene, 3
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