duan_jandClaude Fable 5
c3c38856b3
Main README: clone/SSH/branching quickstart with full /das paths, --tmpdir/--distdir as part of the standard build command (do not fill /var/tmp or $HOME) with cleanup for defaults, tips deduplicated against module READMEs, old-system references removed, resource links and tutorial acknowledgements added. Module READMEs: purge outdated recipes repo-wide — Pmodules/1.1.20 and 2.0.0 plus ./build replaced by modbuild/2.1.3 invocations; the cctbx unbound-variable fix moved from the main README into phenix and DIALS READMEs where it belongs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Xtrapol8
Calculation of Fourier difference maps, extrapolated structure factor amplitudes (ESFAs) and occupancy estimation of low-occupancy triggered states. Built on cctbx; needs licensed Phenix (>=1.19) and CCP4 at runtime.
- Upstream: https://github.com/ElkeDeZitter/Xtrapol8
- License: MIT
How it is built
Upstream installation is just "clone or download, keep all files in one
directory". The recipe downloads the release tag tarball from GitHub and
untars it into $PREFIX/bin. Loading the module sets XTRAPOL8_DIR,
puts $PREFIX/bin on PATH and auto-loads phenix and ccp4.
Note: release tags switched format at 1.2.8 (v.1.2.8 with a dot);
the default urls: matches the new style, so rebuilding <=1.2.5
versions (tagged v1.x.y) would need a per-version urls: override.
Building on Ra
module use unstable && module load modbuild/2.1.3
cd Xtrapol8
modbuild build 1.2.9
module use MX unstable && module load Xtrapol8/1.2.9
Verifying the install
which Fextr.py # -> .../Xtrapol8/<version>/bin
module list # phenix + ccp4 pulled in
phenix.python "$XTRAPOL8_DIR/bin/Fextr.py" # prints the argument list
Installation remarks
March 2026: From v1.2.6 on, seem to work with phenix/1.21 versions. v1.2.8 is compiled with phenix/1.21 version and needs to be tested to see whether it works.
According to Elke de Zitter (as of Spring 2024) Xtrapol8 only runs with the phenix/1.19 version. --> check for new releases...
Runtime tips
The phenix module with be automatically loaded , but in order to open the GUI one has to do:
phenix.python ${XTRAPOL8_DIR}/bin/X8_gui.py
Exectuables in the ${XTRAPOL8_DIR}/bin/ folder are obviously directly callable if the module is loaded... (for instance Fextr.py)