[phenixbb] Integrating Pymol and coot in Phenix

Darin Lory darin.lory at gmail.com
Wed May 29 12:22:29 PDT 2019


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 at ip-10-246-56-216 Projects]$ which python3
/apps/packages/pymol/bin/python3
[s.darin.lory at 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 at ip-10-246-56-216 Projects]$ which python3
/usr/bin/python3
[s.darin.lory at ip-10-246-56-216 Projects]$ python3 --version

[s.darin.lory at ip-10-246-56-216 Projects]$ unset PYTHONPATH
[s.darin.lory at 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 at 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
> Web: https://phenix-online.org
>
>
> On Thu, May 23, 2019 at 2:04 PM Darin Lory <darin.lory at 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
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