Difference between revisions of "CCTBX"

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=Note=
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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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We need someone to make some edits to this page. I don't know anything about CCTBX except what's shown here.
 
  
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=Computational Crystallography Toolbox=
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cctbx and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible.
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[http://cctbx.sourceforge.net CCTBX]
 
  
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==Using With PyMol==
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=== Incentive PyMOL ===
  
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===Roger Dodd's Solution===
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Using cctbx with Incentive PyMOL 2.x should become easier once the cctbx project provides conda packages.
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Some folks were having issues getting CCTBX to work.  Here's one solution.
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See https://github.com/cctbx/cctbx_project/issues/9
  
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I hesitated to post this because I thought someone would have a more elegant solution, but I have got the draw_cell/symmops scripts working
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==== Linux ====
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on windows with cctbx. I have had it working with all versions of PyMOL including the latest betas. I install PyMOL as usual in '''C:\Program
 
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Files\Delano Scientific\PyMOL'''. I also got hold of python 2.4.1 [http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python 2.4.1] and cctbx
 
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[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe CCTBX For Windows With Python 2.4] and installed them to '''C:\python24''' and ''''C:\cctbx_build''' & '''C:\cctbx_sources''', respectively.
 
  
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In order to get things working together, I launch PyMOL with the following batch file:
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Confirmed procedure to get this working on Linux with CCTBX build '''dev-1723''', which is based on conda:
  
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<pre>
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# Download cctbx from http://cci.lbl.gov/cctbx_build/
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@ECHO off
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# Install cctbx: <code>./install --prefix=$HOME/local</code>
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set LIBTBX_DIST_ROOT=C:\cctbx_sources
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# Install [https://repo.continuum.io/miniconda/ Miniconda]
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if not defined PYTHONPATH set PYTHONPATH=
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# Install '''pymol''' with '''conda''' into the '''cctbx environment''':<syntaxhighlight lang="bash">$HOME/miniconda3/bin/conda install -p $HOME/local/cctbx-dev-1723/conda_base -c schrodinger -c conda-forge pymol</syntaxhighlight>
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set
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# Activate cctbx: <code>source $HOME/local/cctbx-dev-1723/cctbx_env.sh</code>
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PYTHONPATH=C:\cctbx_sources\boost_adaptbx;C:\cctbx_sources\scitbx;C:\cctbx_sources\cctbx;C:\cctbx_sources\iotbx;C:\cctbx_build\libtbx;C:\cctbx_sources\libtbx;%PYTHONPATH%
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# Run PyMOL with: <code>cctbx.python -m pymol</code>
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set LIBTBX_BUILD=C:\cctbx_build
 
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set LIBTBX_PYTHON_EXE=C:\Python24\python.exe
 
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if not defined PATH set PATH=
 
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set PATH=C:\cctbx_build\libtbx\bin;C:\cctbx_build\libtbx;%PATH%
 
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set SCITBX_DIST=C:\cctbx_sources\scitbx
 
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set IOTBX_DIST=C:\cctbx_sources\iotbx
 
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set CCTBX_DIST=C:\cctbx_sources\cctbx
 
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set BOOST_ADAPTBX_DIST=C:\cctbx_sources\boost_adaptbx
 
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set LIBTBX_DIST=C:\cctbx_sources\libtbx
 
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if not defined PATHEXT set PATHEXT=
 
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set PATHEXT=.PX;.PY;%PATHEXT%
 
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call "%LIBTBX_PYTHON_EXE%" "%LIBTBX_DIST%\libtbx\assoc_ftype.py"
 
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"C:\Program Files\DeLano Scientific\PyMOL\PyMOLWin.exe"  +2
 
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</pre>
 
  
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Just save as '''PyMOL.bat''' and run it (this is basically the cctbx '''setpaths.bat''' with a pymol command tagged on the end). I hope this helps.
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==== Windows ====
  
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Confirmed procedure to get this working on Windows with CCTBX build '''dev-1725''', which is based on conda:
  
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# Download cctbx from http://cci.lbl.gov/cctbx_build/
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# Extract ZIP file (e.g. to <code>F:\cctbx-installer-dev-1725-intel-windows-x86_64</code>)
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# Install [https://repo.continuum.io/miniconda/ Miniconda]
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# Install '''pymol''' with '''conda''' into the '''cctbx environment''': <code>conda install -p F:\cctbx-installer-dev-1725-intel-windows-x86_64\conda_base -c schrodinger -c conda-forge pymol</code>
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# Activate cctbx: <code>call F:\cctbx-installer-dev-1725-intel-windows-x86_64\cctbx_env.bat</code>
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# Run PyMOL with: <code>cctbx.python -m pymol</code>
  
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=== Robert Campbell's Solution ===
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=== Open-Source PyMOL ===
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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.
 
  
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[[Category:PyMol_Integration|cctbx]]
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I hope this is clear enough!
 
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[[Category:PyMol_Integration|CCTBX]]
 

Revision as of 15:59, 11 May 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

Using cctbx with Incentive PyMOL 2.x should become easier once the cctbx project provides conda packages. See https://github.com/cctbx/cctbx_project/issues/9

Linux

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

  1. Download cctbx from http://cci.lbl.gov/cctbx_build/
  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/cctbx_env.sh
  6. Run PyMOL with: cctbx.python -m pymol

Windows

Confirmed procedure to get this working on Windows with CCTBX build dev-1725, which is based on conda:

  1. Download cctbx from http://cci.lbl.gov/cctbx_build/
  2. Extract ZIP file (e.g. to F:\cctbx-installer-dev-1725-intel-windows-x86_64)
  3. Install Miniconda
  4. Install pymol with conda into the cctbx environment: conda install -p F:\cctbx-installer-dev-1725-intel-windows-x86_64\conda_base -c schrodinger -c conda-forge pymol
  5. Activate cctbx: call F:\cctbx-installer-dev-1725-intel-windows-x86_64\cctbx_env.bat
  6. Run PyMOL with: cctbx.python -m pymol

Open-Source PyMOL

See CCTBX-fedora32.

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