saspy

PyMOL plugin to run ATSAS tools from within PyMOL

Installation

• Install an Open-Source PyMOL version (see below).

• Make sure ATSAS is installed and working.

• Download the saspy.py file from https://raw.githubusercontent.com/emblsaxs/saspy/master/saspy.py

• Create or modify $HOME/.pymolrc.pml by adding the following line:

  os.environ["PATH"] += os.pathsep + "/xxx/yyy/bin:"

  where /xxx/yyy is the path to your local ATSAS installation.

• Start PyMOL

• Go to Plugin->Plugin Manager->Install New Plugin->Install from local file

• Browse to the downloaded saspy.py, select it, and click Open

For more details:

• https://pymolwiki.org/index.php/Plugins
• https://pymolwiki.org/index.php/Pymolrc

Please use PyMOL 2.0 or the Open-Source version

PyMOL 2.0

• PyMOL version 2.0 has been tested and works properly with SASpy.
• It can be downloaded and installed free of charge from:
  • https://pymol.org/2/#download
• It is available for Linux, Mac and Windows.

Open-Source PyMOL

Open-source PyMOL installations:

• Linux - on your terminal type: > sudo apt-get install pymol

  • apt-get is for Debian/Ubuntu, please adapt depending on your distro, more details at:
  • https://pymolwiki.org/index.php/Linux_Install#Open-Source_PyMOL_in_Linux_Distros

• Mac OS X - installation command: > brew install homebrew/science/pymol

  • For more details: https://pymolwiki.org/index.php/MAC_Install#Pre-compiled
  • (please avoid hybrid and other versions, these may not work properly)

• Windows - please follow instructions at:

  • https://pymolwiki.org/index.php/Windows_Install#Open-Source_PyMOL

In case of doubts, bugs, problems or comments please write to: atsas@embl-hamburg.de