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 $HOME) with cleanup for defaults, tips deduplicated against module READMEs, old-system references removed, resource links and tutorial acknowledgements added. Module READMEs: purge outdated recipes repo-wide — Pmodules/1.1.20 and 2.0.0 plus ./build replaced by modbuild/2.1.3 invocations; the cctbx unbound-variable fix moved from the main README into phenix and DIALS READMEs where it belongs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
53 lines
1.8 KiB
Markdown
53 lines
1.8 KiB
Markdown
# Xtrapol8
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Calculation of Fourier difference maps, extrapolated structure factor
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amplitudes (ESFAs) and occupancy estimation of low-occupancy triggered
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states. Built on cctbx; needs licensed Phenix (>=1.19) and CCP4 at runtime.
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- Upstream: https://github.com/ElkeDeZitter/Xtrapol8
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- License: MIT
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## How it is built
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Upstream installation is just "clone or download, keep all files in one
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directory". The recipe downloads the release tag tarball from GitHub and
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untars it into `$PREFIX/bin`. Loading the module sets `XTRAPOL8_DIR`,
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puts `$PREFIX/bin` on `PATH` and auto-loads phenix and ccp4.
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Note: release tags switched format at 1.2.8 (`v.1.2.8` with a dot);
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the default `urls:` matches the new style, so rebuilding <=1.2.5
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versions (tagged `v1.x.y`) would need a per-version `urls:` override.
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## Building on Ra
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```sh
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module use unstable && module load modbuild/2.1.3
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cd Xtrapol8
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modbuild build 1.2.9
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module use MX unstable && module load Xtrapol8/1.2.9
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```
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## Verifying the install
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```sh
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which Fextr.py # -> .../Xtrapol8/<version>/bin
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module list # phenix + ccp4 pulled in
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phenix.python "$XTRAPOL8_DIR/bin/Fextr.py" # prints the argument list
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```
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### Installation remarks
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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.
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According to Elke de Zitter (as of Spring 2024) Xtrapol8 only runs with the phenix/1.19 version.
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--> check for new releases...
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### Runtime tips
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The phenix module with be automatically loaded , but in order to open the GUI one has to do:
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phenix.python ${XTRAPOL8_DIR}/bin/X8_gui.py
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Exectuables in the ${XTRAPOL8_DIR}/bin/ folder are obviously directly callable if the module is loaded... (for instance Fextr.py)
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