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,