I am going to write a comment for every damn IT issue/fix I get...

fixes-found.md

This is an experiment. Is a GitHub Gist comment a good way to log publically how I fixed an installation or similar issue?

See comments

Jupyter decided to stop starting kernels after a pip install in conda base env. Cause: prompt-toolkit-3.0.42 giving error ModuleNotFoundError: No module named 'prompt_toolkit.output' —ipython run, but import raised error. Fix was simply to pip install prompt-toolkit -U to version 3.0.47.
Oddly, this applied to all conda envs.
One environment's kernel was still effe'ed, but fixed when disinstalled and reinstalled possibly due to lack of conda env config vars set PYTHONUSERBASE=$CONDA_PREFIX

APBS does not work out of the box on Rocky Linux 8.10

https://github.com/Electrostatics/apbs/releases/download/v3.4.1/APBS-3.4.1.Linux.zip
$ unzip APBS-3.4.1.Linux.zip
...REDACTED...
$ ./APBS-3.4.1.Linux/bin/apbs pentakaihemimer.relax.pdb 
./APBS-3.4.1.Linux/bin/apbs: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by ./APBS-3.4.1.Linux/bin/apbs)
./APBS-3.4.1.Linux/bin/apbs: /lib64/libpthread.so.0: version `GLIBC_2.30' not found (required by ./APBS-3.4.1.Linux/bin/apbs)
$ ldd --version
ldd (GNU libc) 2.28
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.
$ source /etc/os-release 
$ echo $PRETTY_NAME 
Rocky Linux 8.10 (Green Obsidian)

MacCoot

CCP4 has coot, but why install the whole, when you need a part?
The following is more icky than the value of zeta(3), but CCP4 installation on Mac can be worse:
installing XQuartz traditionally has made my OS glitchier than a Windows machine running pirated software.

brew tap brewsci/bio
brew install coot
 
# find /opt/homebrew -iname '*coot*' --> /opt/homebrew/Cellar/coot/1.1.11_1.reinstall/bin/coot
# but when run it thinks itself in coot/1.1.11_1/
ln -s /opt/homebrew/Cellar/coot/1.1.11_1.reinstall /opt/homebrew/Cellar/coot/1.1.11_1
export COOT_PATH='/opt/homebrew/Cellar/coot/1.1.11_1'
 
# link binaries to folder in PATH
ln -s $COOT_PATH/bin/coot /opt/homebrew/bin/coot
ln -s $COOT_PATH/libexec/MacCoot /opt/homebrew/bin/MacCoot
 
# boost error? Boost installed                                                       
#brew install boost-python3
#brew upgrade boost-python3
# linking it and crossing fingers...
ln -s /opt/homebrew/Cellar/boost-python3/1.87.0_1/lib/libboost_python313.dylib \
      /opt/homebrew/opt/boost-python3/lib/libboost_python312.dylib

Recolor pymol sesh by divergent colors, with chain B darker

brights = ['0xEA4747', '0xEAC147', '0x99EA47', '0x47EA70', '0x47EAEA', '0x4770EA', '0x9947EA', '0xEA47C1']
darks = ['0x890F0F', '0x896B0F', '0x4C890F', '0x0F892D', '0x0F8989', '0x0F2D89', '0x4C0F89', '0x890F6B']
[cmd.color(col, f'chain A and {name}') for col, name in zip(brights, cmd.get_names())]
[cmd.color(col, f'chain B and {name}') for col, name in zip(darks, cmd.get_names())]