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Axel Kohlmeyer
2020-03-10 15:56:11 -04:00
parent e643e88913
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doc/src/Python_examples.rst
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@ -27,10 +27,8 @@ distribution.
| combination of viz\_tool.py and plot.py and gui.py | |
+----------------------------------------------------------------+--------------------------------------------------+
----------
For the viz\_tool.py and vizplotgui\_tool.py commands, replace "tool"
with "gl" or "atomeye" or "pymol" or "vmd", depending on what
visualization package you have installed.
@ -40,13 +38,10 @@ which is included in the pizza sub-directory. See the `Pizza.py doc pages <pizz
.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
Note that for AtomEye, you need version 3, and there is a line in the
scripts that specifies the path and name of the executable. See the
AtomEye WWW pages `here <atomeye_>`_ or `here <atomeye3_>`_ for more details:
.. parsed-literal::
http://mt.seas.upenn.edu/Archive/Graphics/A
@ -54,12 +49,8 @@ AtomEye WWW pages `here <atomeye_>`_ or `here <atomeye3_>`_ for more details:
.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
.. _atomeye3: http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
The latter link is to AtomEye 3 which has the scripting
capability needed by these Python scripts.
@ -68,7 +59,6 @@ open-source version of PyMol in your Python, so that you can import it
from a Python script. See the PyMol WWW pages `here <pymolhome_>`_ or
`here <pymolopen_>`_ for more details:
.. parsed-literal::
http://www.pymol.org
@ -76,22 +66,16 @@ from a Python script. See the PyMol WWW pages `here <pymolhome_>`_ or
.. _pymolhome: http://www.pymol.org
.. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546
The latter link is to the open-source version.
Note that for VMD, you need a fairly current version (1.8.7 works for
me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
variables that have to match the VMD installation on your system.
----------
See the python/README file for instructions on how to run them and the
source code for individual scripts for comments about what they do.