Hi Harry, Can you try creating a new environment with cctbx-base?
conda create -n new_environment -c conda-forge cctbx-base python=3.9 Then activate the environment to test [bkpoon@eeyore:~] conda activate new_environment (new_environment) [bkpoon@eeyore:~] python Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:33) [Clang 13.0.1 ] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scitbx >>> import scitbx.array_family >>> It looks like you are installing cctbx-base into the Anaconda version of python which is from the defaults channel. Mixing packages from different channels does not always work, even though newer packages in the defaults channel tend to be compatible with packages from conda-forge. Also, if you do not need all the packages that come with the standard Anaconda installation, I would recommend the miniconda or miniforge installers for getting the conda tool. As for the PAE format, some updates have just been committed ( https://github.com/cctbx/cctbx_project/pull/775). The latest nightly builds for the cctbx-base conda package will have those. To get them, prepend the "cctbx-nightly" channel to your conda command. conda create -n new_environment -c cctbx-nightly -c conda-forge cctbx-base python=3.9 You should see that the version for cctbx-base is 2022.8a2. I just made an update for conda-forge that does not have those changes, but I can make a point release if it is helpful. If the PAE code or your installation still does not work, please create an issue on GitHub and we can sort it out. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Mon, Aug 1, 2022 at 7:06 AM Harry Powell < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
