<div dir="ltr">Hi Darin,<div><br></div><div>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.</div><div><br></div><div>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 <a href="http://0-coot.state.py">0-coot.state.py</a> 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.</div><div><br></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 23, 2019 at 2:04 PM Darin Lory <<a href="mailto:darin.lory@gmail.com">darin.lory@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">PhenixGurus,<div><br></div><div>I'm trying to get pymol and coot to run as viewers in Phenix 1.15.2-3472-final.</div><div><br></div><div>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".</div><div><br></div><div>I have the executables in the Linux path as per the FAQ.</div><div><br></div><div>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". </div><div><br></div><div>I get this message:</div><div><br></div><div>$ phenix<br>Already checked for new versions in last 24 hours, skipping<br>/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<br></div><div><br></div><div>Then I click on the PyMol button and get this:</div><div><br></div><div>Could not import runpy module<br>Traceback (most recent call last):<br> File "/apps/packages/pymol/lib/python3.7/runpy.py", line 15, in <module><br> import importlib.util<br> File "/apps/packages/pymol/lib/python3.7/importlib/util.py", line 14, in <module><br> from contextlib import contextmanager<br> File "/apps/packages/pymol/lib/python3.7/contextlib.py", line 5, in <module><br> from collections import deque<br> File "/apps/packages/pymol/lib/python3.7/collections/__init__.py", line 27, in <module><br> from reprlib import recursive_repr as _recursive_repr<br> File "/apps/packages/phenix/phenix-1.15.2-3472/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module><br> raise ImportError('This package should not be accessible on Python 3. '<br>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.<br></div><div><br></div><div>$ which coot<br>/apps/packages/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin/coot<br>$ which pymol<br>/apps/packages/pymol/pymol<br>$ which phenix<br>/apps/packages/phenix/phenix-1.15.2-3472/build/bin/phenix<br></div><div><br></div><div>My environment variables are:</div><div><br></div><div>export PHENIX=/apps/packages/phenix<br>export PHENIX_INSTALLER_DATE=080920070957<br>export PHENIX_VERSION=1.3<br>export PHENIX_RELEASE_TAG=final<br>export PHENIX_ENVIRONMENT=1<br>export PHENIX_MTYPE=intel-linux-2.6-x86_64<br>export PHENIX_MVERSION=linux<br>export PHENIX_USE_MTYPE=intel-linux-2.6-x86_64<br>source /apps/packages/phenix/phenix-1.15.2-3472/phenix_env.sh<br></div><div><br></div><div>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<br></div><div><br></div><div>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}<br></div><div><br></div><div>KIndly advise,</div><div><br></div><div><div dir="ltr" class="gmail-m_194976323823205926gmail_signature"><div dir="ltr"><div>-Darin<br></div></div></div></div></div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div>