Hi again, It seems as I'm stuck with using the wrapper cctbx.python. Only one module complains now = Pymol File "PyWAXS.py", line 8, in <module> import pymol ImportError: No module named pymol I have found a fix to the problem in the ccp4 mailing list: modifying the pymol startup script to source the cctbx setpaths.sh but I'm not sure how to implement this solution. Here's what I've tried: In the macports pymol startup script I've added the line: source /Users/magnus/Downloads/cctbx_build/setpaths.sh but I get the same error.... Suggestions? Magnus On 03 Jun 2014, at 20:55, Magnus Andersson wrote:

Hi Luc,

The problem is I have a macports python build that contains all the rest of the modules that I import in this script. Because cctbx is not included in macports I have a separate build for this. Hence I need to call my script as:

/opt/local/bin/python2.7 script.py

I have set the PYTHONPATH in the bash shell:

export PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local

But, it's not working. Any suggestions how to deal with this?

Thanks,

Magnus

On 03 Jun 2014, at 20:47, Luc Bourhis wrote:

...

Hi Magnus,

you need to use the wrappers cctbx.python instead of python as it sets PYTHONPATH correctly so as to add that cctbx_sources/boost.

Best wishes,

Luc

On 3 Jun 2014, at 20:33, Magnus Andersson wrote:

...

Hi,

I've installed the cctbx package from the selfextracting file found in http://cci.lbl.gov/cctbx_build/

but I run into problems when importing cctbx in my python script:

import iotbx.pdb File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py", line 2, in <module> from cctbx.array_family import flex File "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py", line 2, in <module> import scitbx.array_family.flex File "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py", line 2, in <module> import boost.optional # import dependency ImportError: No module named boost.optional

It is flex.py that wants to import boost.optional and does not find it.

However, I find these three files:

optional.hpp optional_fwd.hpp optional_io.hpp

in the following directory:

/Users/magnus/Downloads/cctbx_sources/boost/boost/optional

which suggests that it's present. What am I missing here? I'm using Mac OS X Version 10.9.3 and Python2.7.

Cheers,

Magnus

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Thanks Luc, I have now updated by PYTHONPATH as you suggested: export PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local/bin:/Users/magnus/Downloads/cctbx_build/lib:/Users/magnus/Downloads/cctbx_sources:/Users/magnus/Downloads/cctbx_sources/boost_adaptbx:/Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath:/usr/local/lib , which indeed makes my /opt/local/bin/python2.7 find boost. However, now I get a new error message, which is a little harder to interpret: import iotbx.pdb File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py", line 2, in <module> from cctbx.array_family import flex File "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py", line 2, in <module> import scitbx.array_family.flex File "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py", line 2, in <module> import boost.optional # import dependency File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/optional.py", line 2, in <module> import boost.python File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py", line 57, in <module> ext = import_ext("boost_python_meta_ext") File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py", line 36, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): dlopen(/Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so, 2): Symbol not found: boost::python::objects::function_object(boost::python::objects::py_function const&, std::__1::pair const&) Referenced from: /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so Expected in: /usr/local/lib/libboost_python.dylib in /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so sys.path: /Users/magnus/Documents/TR-WAXS/magnus_testing/PyWAXS /Users/magnus/.venvburrito/lib/python/distribute-0.6.32-py2.7.egg /Users/magnus/.venvburrito/lib/python/virtualenv-1.8.4-py2.7.egg /Users/magnus/.venvburrito/lib/python/virtualenvwrapper-3.6-py2.7.egg /Users/magnus/.venvburrito/lib/python/stevedore-0.8-py2.7.egg /Users/magnus/.venvburrito/lib/python/virtualenv_clone-0.2.4-py2.7.egg /Users/magnus/.venvburrito/lib/python /Users/magnus/Downloads/cctbx_sources /opt/local/bin /Users/magnus/Downloads/cctbx_build/lib /Users/magnus/Downloads/cctbx_sources/boost_adaptbx /Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath /usr/local/lib /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyObjC /Library/Python/2.7/site-packages I don't know how to deal with this - any suggestions? Thanks, Magnus On 03 Jun 2014, at 23:44, Luc Bourhis wrote:

...

Suggestions?

If you want to do it by hand, you need to parrot what cctbx.python does. You need to set the following environment variables:

1. LIBTBX_BUILD that must be the path of cctbx_build next to cctbx_sources or cctbx_project

2. PYTHONPATH at the very least it shall contain $LIBTBX_BUILD/lib:$CCTBXSRC:$CCTBXSRC/boost_adaptbx:$CCTBXSRC/libtbx/pythonpath

where $CCTBXSRC is the full path of cctbx_sources or cctbx_project

3. DYLD_LIBRARY_PATH It shall contain $LIBTBX_BUILD/lib

Best wishes,

Luc

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Hi,
> I think the problem is that it is picking up libboost_python.dylib that was supplied with the system (in /usr/local/lib), and not the one that was used in compilation (in $LIBTBX_BUILD/lib). Could you check that there is a libboost_python.dylib in this directory?

Yes, it's there.

> What happens if you change the search order for the linker (if this was Linux, export DYLIB_LIBRARY_PATH=$LIBTBX_BUILD/lib:$DYLIB_LIBRARY_PATH would work, but on the Mac I do not know).
> 

I assume $LIBTBX_BUILD is /Users/magnus/Downloads/cctbx_build/

in my case,

but what is $DYLIB_LIBRARY_PATH?

> It would probably be easier for you to rebuild the cctbx Python bindings with the Python you want to use, and then all things would work.

I think that's what I'm trying to do. I want to avoid the cctbx wrapper and therefore are launching python from my /opt/local/bin install where I keep all the rest of the modules I need. It is only cctbx that causes trouble. So I try to get "my" python to accept it.

Thanks for you help in this matter - I appreciate it, 

Magnus


> It only takes 10-20 minutes to compile even on a vintage computer.
> 
> BW, Gabor
> 
> On 2014-06-04 13:15, Magnus Andersson wrote:
>> Thanks Luc,
>> I have now updated by PYTHONPATH as you suggested:
>> export
>> PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local/bin:/Users/magnus/Downloads/cctbx_build/lib:/Users/magnus/Downloads/cctbx_sources:/Users/magnus/Downloads/cctbx_sources/boost_adaptbx:/Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath:/usr/local/lib
>> , which indeed makes my /opt/local/bin/python2.7 find boost. However,
>> now I get a new error message, which is a little harder to interpret:
>> import iotbx.pdb
>> File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py",
>> line 2, in 
>> from cctbx.array_family import flex
>> File
>> "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py",
>> line 2, in 
>> import scitbx.array_family.flex
>> File
>> "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py",
>> line 2, in 
>> import boost.optional # import dependency
>> File
>> "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/optional.py",
>> line 2, in 
>> import boost.python
>> File
>> "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py",
>> line 57, in 
>> ext = import_ext("boost_python_meta_ext")
>> File
>> "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py",
>> line 36, in import_ext
>> + [" "+p for p in sys.path]))
>> ImportError: __import__("boost_python_meta_ext"):
>> dlopen(/Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so,
>> 2): Symbol not found:
>> boost::python::objects::function_object(boost::python::objects::py_function
>> const&, std::__1::pair> boost::python::detail::keyword const*> const&)
>> Referenced from:
>> /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so
>> Expected in: /usr/local/lib/libboost_python.dylib
>> in /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so
>> sys.path:
>> /Users/magnus/Documents/TR-WAXS/magnus_testing/PyWAXS
>> /Users/magnus/.venvburrito/lib/python/distribute-0.6.32-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python/virtualenv-1.8.4-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python/virtualenvwrapper-3.6-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python/stevedore-0.8-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python/virtualenv_clone-0.2.4-py2.7.egg
>> /Users/magnus/.venvburrito/lib/python
>> /Users/magnus/Downloads/cctbx_sources
>> /opt/local/bin
>> /Users/magnus/Downloads/cctbx_build/lib
>> /Users/magnus/Downloads/cctbx_sources/boost_adaptbx
>> /Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath
>> /usr/local/lib
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyObjC
>> /Library/Python/2.7/site-packages
>> I don't know how to deal with this - any suggestions?
>> Thanks,
>> Magnus
>> On 03 Jun 2014, at 23:44, Luc Bourhis  wrote:
>>>> Suggestions?
>>> If you want to do it by hand, you need to parrot what cctbx.python
>>> does. You need to set the following environment variables:
>>> 1. LIBTBX_BUILD
>>> that must be the path of cctbx_build next to cctbx_sources or
>>> cctbx_project
>>> 2. PYTHONPATH
>>> at the very least it shall contain
>> $LIBTBX_BUILD/lib:$CCTBXSRC:$CCTBXSRC/boost_adaptbx:$CCTBXSRC/libtbx/pythonpath
>>> where $CCTBXSRC is the full path of cctbx_sources or cctbx_project
>>> 3. DYLD_LIBRARY_PATH
>>> It shall contain $LIBTBX_BUILD/lib
>>> Best wishes,
>>> Luc
>>> _______________________________________________
>>> cctbxbb mailing list
>>> [email protected]
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>> _______________________________________________
>> cctbxbb mailing list
>> [email protected]
>> http://phenix-online.org/mailman/listinfo/cctbxbb
> 
> 
> _______________________________________________
> cctbxbb mailing list
> [email protected]
> http://phenix-online.org/mailman/listinfo/cctbxbb

Ok, now I'm getting a little further at least. But is encounter a new error message, which I don’t understand: import iotbx.pdb File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py", line 2, in <module> from cctbx.array_family import flex File "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py", line 2, in <module> import scitbx.array_family.flex File "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py", line 2, in <module> import boost.optional # import dependency File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/optional.py", line 2, in <module> import boost.python File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py", line 129, in <module> floating_point_exceptions = floating_point_exceptions() File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py", line 122, in floating_point_exceptions import libtbx.load_env File "/Users/magnus/Downloads/cctbx_sources/libtbx/load_env.py", line 5, in <module> libtbx.env = libtbx.env_config.unpickle() File "/Users/magnus/Downloads/cctbx_sources/libtbx/env_config.py", line 2194, in unpickle set_preferred_sys_prefix_and_sys_executable(build_path=build_path) File "/Users/magnus/Downloads/cctbx_sources/libtbx/env_config.py", line 2110, in set_preferred_sys_prefix_and_sys_executable if (op.samefile(build_path, dirname)): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.py", line 162, in samefile s1 = os.stat(f1) OSError: [Errno 2] No such file or directory: '' Somewhere it was suggested to launch by: python ./script.py instead of python script.py but in my case, that didn't help Suggestions how to proceed from here? Thanks, Magnus On 04 Jun 2014, at 15:01, Gabor Bunkoczi wrote:

Hi Magnus,

...

but what is $DYLIB_LIBRARY_PATH?

Sorry, this should be DYLD_LIBRARY_PATH, as suggested by Luc's original answer below.

...

...

It would probably be easier for you to rebuild the cctbx Python bindings with the Python you want to use, and then all things would work. I think that's what I'm trying to do. I want to avoid the cctbx wrapper and therefore are launching python from my /opt/local/bin install where I keep all the rest of the modules I need. It is only cctbx that causes trouble. So I try to get "my" python to accept it.

Yeah, but this may not work if there is some binary incompatibility. So far it looks you are lucky, and it may. If not, you have to rebuild. This will not change "your" python in any way, i.e. other extensions remain functional.

Gabor

...

...

It only takes 10-20 minutes to compile even on a vintage computer. BW, Gabor On 2014-06-04 13:15, Magnus Andersson wrote: Thanks Luc, I have now updated by PYTHONPATH as you suggested: export PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local/bin:/Users/magnus/Downloads/cctbx_build/lib:/Users/magnus/Downloads/cctbx_sources:/Users/magnus/Downloads/cctbx_sources/boost_adaptbx:/Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath:/usr/local/lib , which indeed makes my /opt/local/bin/python2.7 find boost. However, now I get a new error message, which is a little harder to interpret: import iotbx.pdb File "/Users/magnus/Downloads/cctbx_sources/iotbx/pdb/__init__.py", line 2, in <module> from cctbx.array_family import flex File "/Users/magnus/Downloads/cctbx_sources/cctbx/array_family/flex.py", line 2, in <module> import scitbx.array_family.flex File "/Users/magnus/Downloads/cctbx_sources/scitbx/array_family/flex.py", line 2, in <module> import boost.optional # import dependency File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/optional.py", line 2, in <module> import boost.python File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py", line 57, in <module> ext = import_ext("boost_python_meta_ext") File "/Users/magnus/Downloads/cctbx_sources/boost_adaptbx/boost/python.py", line 36, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"):

Thanks for you help in this matter - I appreciate it, Magnus dlopen(/Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so,

...

2): Symbol not found: boost::python::objects::function_object(boost::python::objects::py_function const&, std::__1::pair const&) Referenced from: /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so Expected in: /usr/local/lib/libboost_python.dylib in /Users/magnus/Downloads/cctbx_build/lib/boost_python_meta_ext.so sys.path: /Users/magnus/Documents/TR-WAXS/magnus_testing/PyWAXS /Users/magnus/.venvburrito/lib/python/distribute-0.6.32-py2.7.egg /Users/magnus/.venvburrito/lib/python/virtualenv-1.8.4-py2.7.egg /Users/magnus/.venvburrito/lib/python/virtualenvwrapper-3.6-py2.7.egg /Users/magnus/.venvburrito/lib/python/stevedore-0.8-py2.7.egg /Users/magnus/.venvburrito/lib/python/virtualenv_clone-0.2.4-py2.7.egg /Users/magnus/.venvburrito/lib/python /Users/magnus/Downloads/cctbx_sources /opt/local/bin /Users/magnus/Downloads/cctbx_build/lib /Users/magnus/Downloads/cctbx_sources/boost_adaptbx /Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath /usr/local/lib /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyObjC /Library/Python/2.7/site-packages I don't know how to deal with this - any suggestions? Thanks, Magnus On 03 Jun 2014, at 23:44, Luc Bourhis wrote: Suggestions? If you want to do it by hand, you need to parrot what cctbx.python does. You need to set the following environment variables: 1. LIBTBX_BUILD that must be the path of cctbx_build next to cctbx_sources or cctbx_project 2. PYTHONPATH at the very least it shall contain $LIBTBX_BUILD/lib:$CCTBXSRC:$CCTBXSRC/boost_adaptbx:$CCTBXSRC/libtbx/pythonpath where $CCTBXSRC is the full path of cctbx_sources or cctbx_project 3. DYLD_LIBRARY_PATH It shall contain $LIBTBX_BUILD/lib Best wishes, Luc _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

---

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-- ##################################################

Dr Gabor Bunkoczi

Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ################################################## _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Are you sure LIBTBX_BUILD is set in your environment?

I think so. Here's what I have: export LIBTBX_BUILD=/Users/magnus/Downloads/cctbx_build export PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local/bin:/Users/magnus/Downloads/cctbx_build/lib:/Users/magnus/Downloads/cctbx_sources:/Users/magnus/Downloads/cctbx_sources/boost_adaptbx:/Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath:/usr/local/lib:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 export DYLD_LIBRARY_PATH=/Users/magnus/Downloads/cctbx_build/lib Magnus

Luc

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On 04 Jun 2014, at 16:14, Luc Bourhis wrote:

On 4 Jun 2014, at 16:02, Magnus Andersson wrote:

...

export LIBTBX_BUILD=/Users/magnus/Downloads/cctbx_build

I mean, does that directory exist? If LIBTBX_BUILD was not set, it would have crashed even earlier.

I'm afraid I'm not sure what you mean? The directory /Users/magnus/Downloads/cctbx_build does exist.

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Yes, the three exports are in my .bash_profile I launch by: /opt/local/bin/python2.7 PyWAXS.py where I have my python build that contains all modules I need but type python gives: python is /Library/Frameworks/Python.framework/Versions/2.7/bin/python Any idea of what goes on here? Magnus On 04 Jun 2014, at 18:07, Luc Bourhis wrote:

On 4 Jun 2014, at 17:55, Magnus Andersson wrote:

...

yes, that's empty too. Do you have an idea of how to best proceed?

So you are in terminal: you issue the 3 export's you showed us above, then you do "python some_script.py". Correct? If so, what "type python" tells?

Luc

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ok, you might be on to something here I get nothing: echo $LIBTBX_BUILD even though my bash states: export LIBTBX_BUILD=/Users/magnus/Downloads/cctbx_build export PYTHONPATH=/Users/magnus/Downloads/cctbx_sources:/opt/local/bin:/Users/magnus/Downloads/cctbx_build/lib:/Users/magnus/Downloads/cctbx_sources:/Users/magnus/Downloads/cctbx_sources/boost_adaptbx:/Users/magnus/Downloads/cctbx_sources/libtbx/pythonpath:/usr/local/lib:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 export DYLD_LIBRARY_PATH=/Users/magnus/Downloads/cctbx_build/lib and echo $PATH /opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/magnus/.venvburrito/bin:/sw/lib/cctbx/cctbx_build/bin:/sw/bin:/sw/sbin:/Users/magnus/Downloads/cctbx_build/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin Magnus On 04 Jun 2014, at 21:01, Luc Bourhis wrote:

On 4 Jun 2014, at 19:26, Magnus Andersson wrote:

...

Yes, the three exports are in my .bash_profile

Can you confirm that .bash_profile is sourced when you open a new Terminal window? E.g. what do you get with "echo $LIBTBX_BUILD"? I know I am grasping at straw at this stage…

...

I launch by:

/opt/local/bin/python2.7 PyWAXS.py

where I have my python build that contains all modules I need

but

type python

gives: python is /Library/Frameworks/Python.framework/Versions/2.7/bin/python

Any idea of what goes on here?

"echo $PATH" shall give you the answer to that! But if you launch your script PyWAXS.py with the full path /opt/local/bin/python2.7, it should not matter.

Luc

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Hi Luc, I've been travelling and haven't gotten back to this until now. Still having issues though. And, I received an email from a user with similar problems so it might be worth looking further into this.

On Unixes, .bash_profile is only sourced when you log in but not when you open a new terminal. It is different by default on MacOS X because of the way Terminal.app is configured but if you changed that, then .bash_profile won't be sourced. Try putting your export's in .bashrc instead or open Terminal > Preferences > Startup and select "Shell opens with: Default Login Shell".

I have checked and my exports have been sourced correctly.

...

echo $PATH /opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/magnus/.venvburrito/bin:/sw/lib/cctbx/cctbx_build/bin:/sw/bin:/sw/sbin:/Users/magnus/Downloads/cctbx_build/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

Ok. MacPorts installs python27 but not python, so "type python" gets the system one. You need to do port select --set python27 to get python mapped to /opt/local/bin/python27.

I get: port select --set python27 Error: The 'set' command expects two arguments: <group>, <version> I tried to figure this out but without success... sorry to bug you with syntax issues. Magnus

Luc

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Hi,

Just out of curiosity, what are these other modules?

I doublechecked - it is in fact only PyMOL.

I have found it very straightforward to install PyMOL via the cctbx.python wrapper

Can you explain to a relative Python newbie how this is done? Thanks, Magnus

; for other packages it will depend on how straightforward they are to build (which varies on Mac).

Luc's advice is of course correct, but we generally advise building CCTBX with the Python you plan to use it with if possible. Sometimes this means building the whole mess from source.

-Nat _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb