[phenixbb] Integrating Pymol and coot in Phenix

[Billy Poon]

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
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