Hi Billy Many thanks for this - unfortunately, there are other dependencies that appear not to be included in
> conda create -n new_environment -c conda-forge cctbx-base python=3.9 e.g. > [MacPro:~] harry% conda activate phenix_env > (phenix_env) [MacPro:~] harry% python > Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:52) > [Clang 13.0.1 ] on darwin > Type "help", "copyright", "credits" or "license" for more information. > >>> import scitbx > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/Volumes/Users/harry/.local/lib/python3.9/site-packages/scitbx/__init__.py", > line 1, in <module> > from .manage_yaml import Yaml > File > "/Volumes/Users/harry/.local/lib/python3.9/site-packages/scitbx/manage_yaml.py", > line 1, in <module> > import yaml > ModuleNotFoundError: No module named 'yaml' > >>> (WHAT? No YAML?). I’ll continue this discussion off-BB… Regarding the PAE matrix reader, I wrote my own since I need to read them for other applications. But it’s good to know that (once I get process_predicted_model working) you guys are on the case. Best wishes Harry > On 2 Aug 2022, at 06:52, Billy Poon <bkp...@lbl.gov> wrote: > > 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/
