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Learn-PyMOL-for-Biology-Research-1

Posted on Edited on

Updated in Aug/22/2016

Here I will teach How to set the environment in Mac

  1. (install the Xcode and Xcode-command-tool.)[http://railsapps.github.io/xcode-command-line-tools.html]

  2. (install the MacPort)[https://www.macports.org/install.php]
    update MacPort by this command

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    sudo port -v selfupdate

  3. Tried to install PyMOL by MacPort

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    sudo port install pymol

    And following the tips in the warning to install the python

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    find ~/ -type f -name "_cmd.so"

    eg: return 

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    /opt//local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/_cmd.so

    Try to add the path of folder of pymol in the PYTHONPATH
    eg: /opt//local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/

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    PYTHONPATH="/opt//local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages"
    export PYTHONPATH

Abstract:

This Series of blog pages is about the Script of PyMOL. If you are an expert of PyMOL/Python and give me some suggestions or find some errors in this page, I will be very happpppy. This is my First time to use PyMOL

Since the Dr.Marcelo Marcet-Palacios only provide a exist file of PyMOL software without a PyMOL API for Python. I am starting to setup the environment of Open-Source PyMOL, which take a long time(take care).

Setup Environment.

Dr.Marcelo Marcet-Palacios helped me to install the PyMOL by a Mac-package. However, I found the python script cannot load the PyMOL module. I started to find the reason.

https://www.biostars.org/p/113328/ helps a lot. If you want to

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import pymol

in your script, you wish you can install the pymol following the steps of installing an Open-Source PyMOL.

So I started to follow the http://www.pymolwiki.org/index.php/MAC_Install to install an Open-Source PyMOL. If your mac is over 10.5, my feedback is not use the fink, which is not easy to install.

Try this

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sudo port install tcl -corefoundation
sudo port install tk -quartz

sudo port install pymol

The other issue make me so annoying is that

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Traceback (most recent call last):
  File "/usr/local/Cellar/pymol/1.8.2.1/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 72, in <module>
    import pymol
  File "/usr/local/Cellar/pymol/1.8.2.1/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 536, in <module>
    import pymol._cmd
ImportError: dlopen(/usr/local/Cellar/pymol/1.8.2.1/libexec/lib/python2.7/site-packages/pymol/_cmd.so, 2): Library not loaded: /usr/local/opt/glew/lib/libGLEW.2.0.0.dylib
  Referenced from: /usr/local/Cellar/pymol/1.8.2.1/libexec/lib/python2.7/site-packages/pymol/_cmd.so
  Reason: image not found

I in my

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/usr/local/opt/glew/lib

It only has these following files:

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libGLEW.1.13.0.dylib	libGLEW.dylib		libGLEWmx.a
libGLEW.1.13.dylib	libGLEWmx.1.13.0.dylib	libGLEWmx.dylib
libGLEW.a		libGLEWmx.1.13.dylib	pkgconfig

The brew cannot upgrade the openGL. I have to update the XOs to the newest version. So I am downloading the package for 6 GB.

See you tomorrow. Hopefully, I could setup the environment.

Reference

https://www.biostars.org/p/113328/
http://www.pymolwiki.org/index.php/MAC_Install