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 Module READMEs: purge outdated recipes repo-wide — Pmodules/1.1.20 and 2.0.0 plus ./build replaced by modbuild/2.1.3 invocations; the cctbx unbound-variable fix moved from the main README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>
pymol
Molecular visualization system. This module ships the incentive (official Schrodinger) Linux bundle, not the open-source build.
- Upstream: https://pymol.org/ (support: https://www.pymol.org/support.html)
- License: Schrodinger incentive license required for full features
How it is built
Per pymol.org support page for Linux (RHEL 8+ supported since v2.5.10):
download the PyMOL-<ver>_<build>-Linux-x86_64-py310.tar.bz2 bundle,
unpack, run ./pymol. The recipe downloads the bundle from the public
pymol-storage GCS bucket (sha256-verified), unpacks it and moves the
bundle contents into $PREFIX; the pymol launcher sits at the PREFIX
root, so the modulefile does prepend-path PATH $PREFIX (the bundle's
private bin/ with its own python is deliberately NOT on PATH).
Versions before 3.1.8 in this module's git history were open-source builds (git clone + setup.py) against merlin-era psi-python modules; see https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL if that route is ever needed again.
License file
The bundle runs unlicensed with limited features. Site-wide: drop the
SLM license file at $PREFIX/share/pymol/license.lic. Per user: PyMOL
prompts on first start (get the file from https://pymol.org/dsc/ip/license/).
Building on Ra
module use unstable && module load modbuild/2.1.3
cd pymol
modbuild build 3.1.8
module use MX unstable && module load pymol/3.1.8
Verifying the install
which pymol # -> /opt/psi/MX/pymol/3.1.8/pymol
pymol -cq # headless no-op: exits 0 without X
pymol # GUI check, needs X
Adding a new version
Check the exact bundle filename on https://pymol.org (the _0 build
number and py310 tag change between releases), update urls: if
needed, add the version + tarball sha256 in files/config.yaml, then
modbuild build <version> (modbuild/2.1.3) on a Ra login node.