Difference between revisions of "CCTBX"

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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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[http://cctbx.sourceforge.net cctbx]
 
  
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==Using With PyMol==
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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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===On a Mac===
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=== Incentive PyMOL ===
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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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 +
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:
 +
 
 +
# Download cctbx from http://cci.lbl.gov/cctbx_build/
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# Install cctbx: <code>./install --prefix=$HOME/local</code>
 +
# Install [https://repo.continuum.io/miniconda/ Miniconda]
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# Install '''pymol''' with '''conda''' into the '''cctbx environment''':<syntaxhighlight lang="bash">$HOME/miniconda3/bin/conda install -p $HOME/local/cctbx-dev-1723/conda_base -c schrodinger -c conda-forge pymol</syntaxhighlight>
 +
# 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>
 +
 
 +
==== Windows ====
 +
 
 +
Confirmed procedure to get this working on Windows with CCTBX build '''dev-1725''', which is based on conda:
 +
 
 +
# Download cctbx from http://cci.lbl.gov/cctbx_build/
 +
# Extract ZIP file (e.g. to <code>F:\cctbx-installer-dev-1725-intel-windows-x86_64</code>)
 +
# Install [https://repo.continuum.io/miniconda/ Miniconda]
 +
# 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>
 +
# Activate cctbx: <code>call F:\cctbx-installer-dev-1725-intel-windows-x86_64\cctbx_env.bat</code>
 +
# Run PyMOL with: <code>cctbx.python -m pymol</code>
 +
 
 +
=== Open-Source PyMOL ===
 +
 
 +
Confirmed procedure to get this working on Linux: Compile PyMOL with <code>cctbx.python</code>
 +
 
 +
Current cctbx builds neither include PyQt, nor a working Tkinter module. These need to be compiled from source if needed.
 +
 
 +
# Download cctbx from http://cci.lbl.gov/cctbx_build/
 +
# Install cctbx: <code>./install --prefix=$HOME/local</code>
 +
# Activate cctbx: <code>source $HOME/local/cctbx-dev-1658/cctbx_env.sh</code>
 +
# Compile PyMOL with: <code>cctbx.python setup.py --glut install</code> (see [[Linux Install]] for details)
 +
# Install Pmw from https://github.com/schrodinger/pmw-patched with: <code>cctbx.python setup.py install</code>
 +
# 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>
 +
 
 +
<div style="padding: 20px; margin-top:40px; background-color: #f90;">
 +
The following instructions are outdated and might not work anymore
 +
</div>
  
 
===Windows XP (Roger Dodd)===
 
===Windows XP (Roger Dodd)===
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C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)
 
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)
  
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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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[http://cci.lbl.gov/cctbx_build/ cctbx]
  
 
3. Download pymol built against python 2.4 (but not including its own
 
3. Download pymol built against python 2.4 (but not including its own
 
python) and install in the default location
 
python) and install in the default location
  
−
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]
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[http://delsci.com/rel/098/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]
  
−
(You cannot use the latest beta versions which include their own version
+
(Newer versions of PyMOL linked against an external python are available from Delano Scientific on request for holders of a valid subscription.)
−
of python to the best of my knowledge)
 
  
 
4. Create 2 files (use notepad or wordpad or any other text editor) and
 
4. Create 2 files (use notepad or wordpad or any other text editor) and
Line 35: Line 79:
 
     a) pymol.cmd
 
     a) pymol.cmd
  
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       @python -x "%~f0" %* & exit /b
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       @cctbx.python -x "%~f0" %* & exit /b
 
         import cctbx
 
         import cctbx
 
         import pymol
 
         import pymol

Revision as of 05:20, 2 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 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

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 http://cci.lbl.gov/cctbx_build/
  2. Install cctbx: ./install --prefix=$HOME/local
  3. Activate cctbx: source $HOME/local/cctbx-dev-1658/cctbx_env.sh
  4. Compile PyMOL with: cctbx.python setup.py --glut install (see Linux Install for details)
  5. Install Pmw from https://github.com/schrodinger/pmw-patched with: cctbx.python setup.py install
  6. Install _tkinter.so:
    1. Download Python-2.7 source from https://www.python.org/downloads/release/python-2715/
    2. cd Python-2.7.15/Modules
    3. Download https://pymol.org/tmp/setup_tkinter_cctbx.py
    4. cctbx.python setup_tkinter_cctbx.py 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)

Python-2.4.1

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

Numarray-1.3.3

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

cctbx

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

pymol-0_98rc5

(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 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: 

/usr/bin/python  $PYMOL_PATH/modules/launch_pymol.py $*

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: 

python  $PYMOL_PATH/modules/launch_pymol.py $*

(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.

Within pymol, type the command: 

print sys.path

and you should now see the cctbx directories show up.

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