Difference between revisions of "Running Scripts"
(Help for running pymol and python scripts for beginners)
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Revision as of 06:05, 5 August 2010
Saving the source code
First, you have to save the source code. Copy the text in the box to a text editor and save it in text format under an arbitrary file name, let's say we save it as script.txt in the PyMOL working directory.
Python or Pymol?
Then, you have to find out wheter the script you want to run is a python script or a PyMOL script. Look at the source code: if the lines look just as you type them in the command line in PyMOL, it is a PyMOL script. Run it with @, in our example, type
in the PyMOL command line. You can find examples in the script library: Split_Movement (loads a structure from the internet and moves parts in different directions), Show_charged (Selects charged residues and highlights them). Any PyMOL log file would also be an example for a pymol script.
If, in contrast, you find words as "import" in one of the first lines, or "def" or "cmd" in the text body, you have a python script. Run it with run. In the example, type
in the PyMOL command line.
Most python scripts in the script library don't start action immediately but define a new command instead. You first have to run the script and then you can use the command. Many script pages provide hints for usage. If not, look at the bottom of the script for a line like this:
The text in quotation marks is the new command. Enter it in the PyMOL command line.
PyMOL>run color_obj.py PyMOL>color_obj Colouring objects using PyMOL defined colours obj_0001 red obj_0002 green obj_0003 blue obj_0004 yellow obj_0005 violet obj_0006 cyan obj_0007 salmon obj_0008 lime obj_0009 pink obj_0010 slate obj_0011 magenta obj_0012 orange obj_0013 marine obj_0014 olive ...