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
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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]