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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===On a Mac===
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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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There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac].  Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].
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See https://github.com/cctbx/cctbx_project/issues/9
  
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===Windows XP (Roger Dodd)===
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==== Linux ====
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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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Confirmed procedure to get this working on Linux with CCTBX build '''dev-1723''', which is based on conda:
  
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1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
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# Download cctbx from http://cci.lbl.gov/cctbx_build/
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scripts you also need to install numarray after installing python
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# Install cctbx: <code>./install --prefix=$HOME/local</code>
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# Install [https://repo.continuum.io/miniconda/ Miniconda]
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# Install '''pymol''' with '''conda''' into the '''cctbx environment''':<syntaxhighlight lang="bash">$HOME/miniconda3/bin/conda install -p $HOME/local/cctbx-dev-1723/conda_base -c schrodinger -c conda-forge pymol</syntaxhighlight>
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# Activate cctbx: <code>source $HOME/local/cctbx-dev-1723/cctbx_env.sh</code>
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# Run PyMOL with: <code>cctbx.python -m pymol</code>
  
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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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==== Windows ====
  
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2. Download cctbx *without* python included and unpack into
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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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C:\cctbx_build and C:\cctbx_sources
 
  
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[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]
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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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3. Download pymol built against python 2.4 (but not including its own
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# Install [https://repo.continuum.io/miniconda/ Miniconda]
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python) and install in the default location
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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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[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]
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# Run PyMOL with: <code>cctbx.python -m pymol</code>
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(You cannot use the latest beta versions which include their own version
 
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of python to the best of my knowledge)
 
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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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      @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. One other thing, it's important to have python in your path variable
 
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(which you can access by going to control
 
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panel|system|advanced|environment variables), just add C:\python24 to
 
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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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print sys.path
 
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and you should now see the cctbx directories show up.
 
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I hope this is clear enough!
 
  
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=== Open-Source PyMOL ===
  
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See [[CCTBX-fedora32]].
  
 
[[Category:PyMol_Integration|cctbx]]
 
[[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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