Billy,

Thank you very much for the details.  I created a modulefile for PyMol and I set these variables.  I've also opened a ticket with Schrodinger about Pymol variables. They told me this:

Thanks for reaching out! There shouldn't be a need for defining other environment variables when setting up PyMOL via modules. Occasionally there are PYTHON_PATH conflicts and python2/3 inconsistencies in the system paths that need resolving but with the anaconda distribution those are more rare these days.

As for integrating with Phenix - I unfortunately do not have any experience with this. Are there specific issues you are running into there?

PyMol variables:

PATH=/apps/packages/pymol/bin:/usr/lib64/ccache:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin
PYMOL_HOME=/apps/packages/pymol/bin

# which pymol
/apps/packages/pymol/bin/pymol
# which python3
/apps/packages/pymol/bin/python3
# python3 --version
Python 3.7.3
# which conda
/apps/packages/pymol/bin/conda
# conda --version
conda 4.6.14

Here are the issues I'm having:

++++++++++++++++
Phenix run WITH PyMol variables:
++++++++++++++++

$ phenix
Could not import runpy module
Traceback (most recent call last):
  File "/apps/packages/pymol/lib/python3.7/runpy.py", line 15, in <module>
    import importlib.util
  File "/apps/packages/pymol/lib/python3.7/importlib/util.py", line 14, in <module>
    from contextlib import contextmanager
  File "/apps/packages/pymol/lib/python3.7/contextlib.py", line 5, in <module>
    from collections import deque
  File "/apps/packages/pymol/lib/python3.7/collections/__init__.py", line 27, in <module>
    from reprlib import recursive_repr as _recursive_repr
  File "/apps/packages/phenix/phenix-1.15.2-3472/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module>
    raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.

Python 3 for PyMol:
[s.darin.lory@ip-10-246-56-216 Projects]$ which python3
/apps/packages/pymol/bin/python3
[s.darin.lory@ip-10-246-56-216 Projects]$ python3 --version
Python 3.7.3

++++++++++++++++
Phenix run WITHOUT PyMol variables:
++++++++++++++++

$ phenix
Already checked for new versions in last 24 hours, skipping
Could not import runpy module
Traceback (most recent call last):
  File "/apps/packages/pymol/lib/python3.7/runpy.py", line 15, in <module>
    import importlib.util
  File "/apps/packages/pymol/lib/python3.7/importlib/util.py", line 14, in <module>
    from contextlib import contextmanager
  File "/apps/packages/pymol/lib/python3.7/contextlib.py", line 5, in <module>
    from collections import deque
  File "/apps/packages/pymol/lib/python3.7/collections/__init__.py", line 27, in <module>
    from reprlib import recursive_repr as _recursive_repr
  File "/apps/packages/phenix/phenix-1.15.2-3472/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module>
    raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.
Python 3.6.8

Python 3 for Phenix:
[s.darin.lory@ip-10-246-56-216 Projects]$ which python3
/usr/bin/python3
[s.darin.lory@ip-10-246-56-216 Projects]$ python3 --version

[s.darin.lory@ip-10-246-56-216 Projects]$ unset PYTHONPATH
[s.darin.lory@ip-10-246-56-216 Projects]$ phenix
Already checked for new versions in last 24 hours, skipping
Could not import runpy module
Traceback (most recent call last):
  File "/apps/packages/pymol/lib/python3.7/runpy.py", line 15, in <module>
    import importlib.util
  File "/apps/packages/pymol/lib/python3.7/importlib/util.py", line 14, in <module>
    from contextlib import contextmanager
  File "/apps/packages/pymol/lib/python3.7/contextlib.py", line 5, in <module>
    from collections import deque
  File "/apps/packages/pymol/lib/python3.7/collections/__init__.py", line 27, in <module>
    from reprlib import recursive_repr as _recursive_repr
  File "/apps/packages/phenix/phenix-1.15.2-3472/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module>
    raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.

I had found this: https://stackoverflow.com/questions/42214414/this-package-should-not-be-accessible-on-python-3-when-running-python3/43316534

Best regards,

-Darin

On Thu, May 23, 2019 at 7:31 PM Billy Poon <BKPoon@lbl.gov> wrote:
Hi Darin,

For PyMol, it looks like they are using Python 3.7. We are working on moving Phenix to Python 3, so we are currently still on Python 2.7. There are many changes between Python 2 and 3, so that would be to cause of the incompatibility. You should be able to open a model and map from Phenix with the new PyMol, it is the integration between the Phenix GUI and PyMol that will be missing.

For Coot, does type "coot" on the command-line work normally? It seems odd that coot is looking for that file in the "bin" directory. That file is normally output when you quit Coot and it writes out some files for restoring the state. Do you have other files like 0-coot-history.scm or 0-coot.state.py in the "bin" directory? You could try deleting them and starting coot again. Also, you can turn off the creation of these files by adding the "--no-guano" flag.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909


On Thu, May 23, 2019 at 2:04 PM Darin Lory <darin.lory@gmail.com> wrote:
PhenixGurus,

I'm trying to get pymol and coot to run as viewers in Phenix 1.15.2-3472-final.

I have PyMol version 2.3.2 installed and coot 0.8.9.1 "coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python".

I have the executables in the Linux path as per the FAQ.

When I click on the coot button I get another window "Coot is being started with Phenix extentions pre-loaded. Depending on the computer speed, it may take several seconds for the program to open".  

I get this message:

$ phenix
Already checked for new versions in last 24 hours, skipping
/apps/packages/phenix/phenix-1.15.2-3472/build/../modules/phenix/phenix/command_line/start_coot.sh: line 37: /apps/packages/coot-installer/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin/0-coot-history.py: No such file or directory

Then I click on the PyMol button and get this:

Could not import runpy module
Traceback (most recent call last):
  File "/apps/packages/pymol/lib/python3.7/runpy.py", line 15, in <module>
    import importlib.util
  File "/apps/packages/pymol/lib/python3.7/importlib/util.py", line 14, in <module>
    from contextlib import contextmanager
  File "/apps/packages/pymol/lib/python3.7/contextlib.py", line 5, in <module>
    from collections import deque
  File "/apps/packages/pymol/lib/python3.7/collections/__init__.py", line 27, in <module>
    from reprlib import recursive_repr as _recursive_repr
  File "/apps/packages/phenix/phenix-1.15.2-3472/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module>
    raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.

$ which coot
/apps/packages/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin/coot
$ which pymol
/apps/packages/pymol/pymol
$ which phenix
/apps/packages/phenix/phenix-1.15.2-3472/build/bin/phenix

My environment variables are:

export PHENIX=/apps/packages/phenix
export PHENIX_INSTALLER_DATE=080920070957
export PHENIX_VERSION=1.3
export PHENIX_RELEASE_TAG=final
export PHENIX_ENVIRONMENT=1
export PHENIX_MTYPE=intel-linux-2.6-x86_64
export PHENIX_MVERSION=linux
export PHENIX_USE_MTYPE=intel-linux-2.6-x86_64
source /apps/packages/phenix/phenix-1.15.2-3472/phenix_env.sh

export PATH=${PATH}:${APPS_ROOT}/pymol:${APPS_ROOT}/pymol/bin:${APPS_ROOT}/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin:/usr/local/cuda-10.0/lib64:/usr/local/bin

export LD_LIBRARY_PATH=${APPS_ROOT}/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/lib:/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/lib:/usr/local/lib64:/usr/local/lib:${APPS_ROOT}/cryoEF_v1.1.0/lib:/usr/local/relion3/lib:${LD_LIBRARY_PATH}

KIndly advise,

-Darin
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