CCTBX

Note

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

Using With PyMol

On a Mac

There is a page on the cctbx with special instructions for using it on the Mac CCTBX On Mac. Note that you need to use the "Framework" build of PyMOL FrameWorkPyMol.

Roger Dodd's Solution

Some folks were having issues getting CCTBX to work. Here's one solution.

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 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 Files\Delano Scientific\PyMOL. I also got hold of python 2.4.1 Python 2.4.1 and cctbx CCTBX For Windows With Python 2.4 and installed them to C:\python24 and 'C:\cctbx_build & C:\cctbx_sources, respectively.

In order to get things working together, I launch PyMOL with the following batch file:

@ECHO off
set LIBTBX_DIST_ROOT=C:\cctbx_sources
if not defined PYTHONPATH set PYTHONPATH=
set
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%
set LIBTBX_BUILD=C:\cctbx_build
set LIBTBX_PYTHON_EXE=C:\Python24\python.exe
if not defined PATH set PATH=
set PATH=C:\cctbx_build\libtbx\bin;C:\cctbx_build\libtbx;%PATH%
set SCITBX_DIST=C:\cctbx_sources\scitbx
set IOTBX_DIST=C:\cctbx_sources\iotbx
set CCTBX_DIST=C:\cctbx_sources\cctbx
set BOOST_ADAPTBX_DIST=C:\cctbx_sources\boost_adaptbx
set LIBTBX_DIST=C:\cctbx_sources\libtbx
if not defined PATHEXT set PATHEXT=
set PATHEXT=.PX;.PY;%PATHEXT%
call "%LIBTBX_PYTHON_EXE%" "%LIBTBX_DIST%\libtbx\assoc_ftype.py"
"C:\Program Files\DeLano Scientific\PyMOL\PyMOLWin.exe"  +2

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.

Robert Campbell's Solution

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!