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Revision as of 03:11, 1 April 2019

This page describes how to use the Computational Crystallography Toolbox (cctbx) with PyMOL.

cctbx and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible.

Incentive PyMOL

Using cctbx with Incentive PyMOL 2.x should become easier once the cctbx project provides conda packages. See

Confirmed procedure to get this working on Linux with CCTBX build dev-1723, which is based on conda:

  1. Download cctbx from
  2. Install cctbx: ./install --prefix=$HOME/local
  3. Install Miniconda
  4. Install pymol with conda into the cctbx environment:
    $HOME/miniconda3/bin/conda install -p $HOME/local/cctbx-dev-1723/conda_base -c schrodinger -c conda-forge pymol
  5. Activate cctbx: source $HOME/local/cctbx-dev-1723/
  6. Run PyMOL with: cctbx.python -m pymol

Open-Source PyMOL

Confirmed procedure to get this working on Linux: Compile PyMOL with cctbx.python

Current cctbx builds neither include PyQt, nor a working Tkinter module. These need to be compiled from source if needed.

  1. Download cctbx from
  2. Install cctbx: ./install --prefix=$HOME/local
  3. Activate cctbx: source $HOME/local/cctbx-dev-1658/
  4. Compile PyMOL with: cctbx.python --glut install (see Linux Install for details)
  5. Install Pmw from with: cctbx.python install
  6. Install
    1. Download Python-2.7 source from
    2. cd Python-2.7.15/Modules
    3. Download
    4. cctbx.python install
  7. Run PyMOL with: cctbx.python -m pymol

The following instructions are outdated and might not work anymore

Windows XP (Roger Dodd)

1. Download and install python (to the default location - C:\Python24)


1a. If you want to use the or scripts you also need to install numarray after installing python


2. Download cctbx *without* python included and unpack into C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)


3. Download pymol built against python 2.4 (but not including its own python) and install in the default location


(Newer versions of PyMOL linked against an external python are available from Delano Scientific on request for holders of a valid subscription.)

4. Create 2 files (use notepad or wordpad or any other text editor) and save in the C:\Program Files\Delano Scientific\PyMOL directory:

   a) pymol.cmd
      @cctbx.python -x "%~f0" %* & exit /b
       import cctbx
       import pymol
   b) run.cmd
       CALL C:\cctbx_build\setpaths_all.bat
       CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. It's important to have python in your path variable (which you can access by going to control panel|system|advanced|environment variables), just add C:\python24 to the end of the path variable, separated by a semi-colon.

Linux (Robert Campbell)

When you run the script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:

/usr/bin/python  $PYMOL_PATH/modules/ $*

in your file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:

python  $PYMOL_PATH/modules/ $*

(assuming you've already run the script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your file or some other file that you source before

Within pymol, type the command:

print sys.path

and you should now see the cctbx directories show up.