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

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())]