Hi folks
No doubt someone will tell me that I should be posting this on the Phenix BB,
but since everyone on there reads ccp4BB as well (:-)), I’m likely to reach the
right audience anyway!
Two Qs -
(1) most important - scitbx.array_family seems to have disappeared (see stuff
below Q2).
(2) Does process_predicted_model.py (when I get it working) read the new-style
PAE matrices that Sameer told us about last week?
Since “upgrading” my conda env so that I am using Python 3.9, I’m getting an
error with “process_predicted_model”, which is used for splitting up AlphaFold
models into (cough, cough) “domains”, based on the PAE matrix. It ran before I
did the move from Python 3.7.something…
I had to remove and reinstall conda to upgrade because I managed to screw up
the environment (and didn’t notice that the Python I was using wasnot actually
the conda one…). So this is on a freshly installed conda...
The error I get when trying to run process_predicted_model.py is -
> [MacPro:~/icl/test] harry% python3 process_predicted_model.py
> pae/AF-Q8W3K0-F1-predicted_aligned_error_v2.json
> Traceback (most recent call last):
> File "/Volumes/Users/harry/icl/test/process_predicted_model.py", line 14,
> in <module>
> from scitbx.array_family import flex
> ModuleNotFoundError: No module named ‘scitbx.array_family'
I’ve tried things like -
conda install -c conda-forge cctbx-base
which installs a load of useful stuff, but not, apparently, scitbx.array_family
-
> Python 3.9.12 (main, Jun 1 2022, 06:36:29)
> [Clang 12.0.0 ] :: Anaconda, Inc. on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scitbx
> >>> import scitbx.array_family
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ModuleNotFoundError: No module named ‘scitbx.array_family'
What do I need to do to get this working? Go back to Python 3.7?
Harry
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