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=Computational Crystallography Toolbox=
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This page describes how to use the [https://github.com/cctbx/cctbx_project Computational Crystallography Toolbox (cctbx)] with PyMOL.
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https://github.com/cctbx/cctbx_project
 
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==Using With PyMol==
 
  
 
cctbx and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible.
 
cctbx and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible.
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=== Incentive PyMOL ===
 
=== Incentive PyMOL ===
  
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Using cctbx with Incentive PyMOL 2.x should be possible once the cctbx project provides conda packages.
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Create a [https://repo.continuum.io/miniconda/ conda] environment with [https://anaconda.org/schrodinger/pymol schrodinger::pymol] and [https://anaconda.org/conda-forge/cctbx-base conda-forge::cctbx-base].
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See https://github.com/cctbx/cctbx_project/issues/9
 
  
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=== Open-Source PyMOL ===
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On Linux and Windows:
  
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Confirmed procedure to get this working on Linux: Compile PyMOL with <code>cctbx.python</code>
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<syntaxhighlight lang="bash">conda create -n env1 schrodinger::pymol conda-forge::cctbx-base</syntaxhighlight>
  
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Current cctbx builds neither include PyQt, nor a working Tkinter module. These need to be compiled from source if needed.
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On macOS, you also need [https://anaconda.org/schrodinger/pymol schrodinger::tk] and [https://www.xquartz.org/ XQuartz]:
  
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# Download cctbx from http://cci.lbl.gov/cctbx_build/
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<syntaxhighlight lang="bash">conda create -n env1 schrodinger::pymol conda-forge::cctbx-base schrodinger::tk</syntaxhighlight>
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# Install cctbx: <code>./install --prefix=$HOME/local</code>
 
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# Activate cctbx: <code>source $HOME/local/cctbx-dev-1658/cctbx_env.sh</code>
 
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# Compile PyMOL with: <code>cctbx.python setup.py --glut install</code> (see [[Linux Install]] for details)
 
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# Install Pmw from https://github.com/schrodinger/pmw-patched with: <code>cctbx.python setup.py install</code>
 
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# Install <code>_tkinter.so</code>:
 
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## Download Python-2.7 source from https://www.python.org/downloads/release/python-2715/
 
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## <code>cd Python-2.7.15/Modules</code>
 
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## Download https://pymol.org/tmp/setup_tkinter_cctbx.py
 
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## <code>cctbx.python setup_tkinter_cctbx.py install</code>
 
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# Run PyMOL with: <code>cctbx.python -m pymol</code>
 
  
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<div style="padding: 20px; margin-top:40px; background-color: #f90;">
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=== Open-Source PyMOL ===
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The following instructions are outdated and might not work anymore
 
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</div>
 
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===Windows XP (Roger Dodd)===
 
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1. Download and install python (to the default location - C:\Python24)
 
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[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]
 
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1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
 
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scripts you also need to install numarray after installing python
 
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[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]
 
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2. Download cctbx *without* python included and unpack into
 
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C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)
 
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[http://cci.lbl.gov/cctbx_build/ cctbx]
 
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3. Download pymol built against python 2.4 (but not including its own
 
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python) and install in the default location
 
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[http://delsci.com/rel/098/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]
 
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(Newer versions of PyMOL linked against an external python are available from Delano Scientific on request for holders of a valid subscription.)
 
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4. Create 2 files (use notepad or wordpad or any other text editor) and
 
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save in the C:\Program Files\Delano Scientific\PyMOL directory:
 
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    a) pymol.cmd
 
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      @cctbx.python -x "%~f0" %* & exit /b
 
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        import cctbx
 
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        import pymol
 
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    b) run.cmd
 
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        CALL C:\cctbx_build\setpaths_all.bat
 
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        CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"
 
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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.
 
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===Linux (Robert Campbell)===
 
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When you run the setpaths.sh 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:
 
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/usr/bin/python  $PYMOL_PATH/modules/launch_pymol.py $*
 
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in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
 
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python  $PYMOL_PATH/modules/launch_pymol.py $*
 
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(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.
 
  
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Within pymol, type the command:
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See [[CCTBX-fedora32]].
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print sys.path
 
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and you should now see the cctbx directories show up.
 
  
 
[[Category:PyMol_Integration|cctbx]]
 
[[Category:PyMol_Integration|cctbx]]

Latest revision as of 04:05, 7 December 2020

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

Create a conda environment with schrodinger::pymol and conda-forge::cctbx-base.

On Linux and Windows: 

conda create -n env1 schrodinger::pymol conda-forge::cctbx-base

On macOS, you also need schrodinger::tk and XQuartz: 

conda create -n env1 schrodinger::pymol conda-forge::cctbx-base schrodinger::tk

Open-Source PyMOL

See CCTBX-fedora32.

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