PyLink

a PyMOL plugin to identify links

VERSION: 1.3 Compatible with Python 3 and PyMOL 2.x Updated on 25.05.2021

The PYMOL PyLink plugin requires the following Python packages. Make sure they are installed before installing this plugin in pymol:

numpy
matplotlib
pmw

These packages may be installed using the following commands.

pip3 install -r requirements.txt

Details @ pylink.cent.uw.edu.pl

Install plugin in PyMOL

Open PyMOL and go to:

plugin -> plugin manager -> install new plugin -> choose file

Select the

__init__.py 

file from the decompressed folder containing the downloaded PyLasso plugin.

Problem with outdated Python pmw package

If you see the following error after opening PyMOL:

Traceback (innermost last):
  File "C:\Python38\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py", line 1776, in __call__
    return self.func(*args)
  File "C:\Python38\lib\site-packages\pymol\plugins\legacysupport.py", line 85, in plugin_manager
    managergui.manager_dialog()
  File "C:\Python38\lib\site-packages\pymol\plugins\managergui.py", line 43, in manager_dialog
    dialog = PluginManager(get_tk_root())
  File "C:\Python38\lib\site-packages\pymol\plugins\managergui.py", line 125, in __init__
    notebook = Pmw.NoteBook(master)
  File "C:\Python38\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py", line 60, in __init__
    Pmw.Color.bordercolors(self, self['hull_background'])
  File "C:\Python38\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py", line 359, in bordercolors
    '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
TypeError: %x format: an integer is required, not float

that means you have an old version of the Python PMW package. You need to install the patched one from:

https://github.com/schrodinger/pmw-patched

PyMOL on Mac OS:

This setup was tested on Mac OS X 11.4 (Big Sur)

Install Xquartz from: https://www.xquartz.org/

Install PyMOL using MacPorts (https://www.macports.org/)

sudo port install pymol py39-matplotlib py39-pmw

After installation close the terminal and open a new one Then start PyMOL by typing:

pyymol