CCTBX: Difference between revisions

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=Note=
This page describes how to use the [https://github.com/cctbx/cctbx_project Computational Crystallography Toolbox (cctbx)] with PyMOL.
We need someone to make some edits to this page. I don't know anything about cctbx except what's shown here.


=Computational Crystallography Toolbox=
cctbx and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible.
[http://cctbx.sourceforge.net cctbx]


==Using With PyMol==
=== Incentive PyMOL ===


===On a Mac===
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].
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].


===Windows XP (Roger Dodd)===
On Linux and Windows:
1. Download and install python (to the default location - C:\Python24)


[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]
<syntaxhighlight lang="bash">conda create -n env1 schrodinger::pymol conda-forge::cctbx-base</syntaxhighlight>


1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
On macOS, you also need [https://anaconda.org/schrodinger/pymol schrodinger::tk] and [https://www.xquartz.org/ XQuartz]:
scripts you also need to install numarray after installing python


[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]
<syntaxhighlight lang="bash">conda create -n env1 schrodinger::pymol conda-forge::cctbx-base schrodinger::tk</syntaxhighlight>


2. Download cctbx *without* python included and unpack into
=== Open-Source PyMOL ===
C:\cctbx_build and C:\cctbx_sources


[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]
See [[CCTBX-fedora32]].


3. Download pymol built against python 2.4 (but not including its own
[[Category:PyMol_Integration|cctbx]]
python) and install in the default location
 
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]
 
(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)
 
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
 
      @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. One other thing, 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.
 
 
I hope this is clear enough!
 
 
 
[[Category:PyMol_Integration|CCTBX]]

Latest revision as of 04:22, 24 September 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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