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 $HOME) with cleanup for defaults, tips deduplicated against module READMEs, old-system references removed, resource links and tutorial acknowledgements added. Module READMEs: purge outdated recipes repo-wide — Pmodules/1.1.20 and 2.0.0 plus ./build replaced by modbuild/2.1.3 invocations; the cctbx unbound-variable fix moved from the main README into phenix and DIALS READMEs where it belongs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
53 lines
1.9 KiB
Markdown
53 lines
1.9 KiB
Markdown
# pymol
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Molecular visualization system. This module ships the **incentive**
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(official Schrodinger) Linux bundle, not the open-source build.
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- Upstream: https://pymol.org/ (support: https://www.pymol.org/support.html)
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- License: Schrodinger incentive license required for full features
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## How it is built
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Per pymol.org support page for Linux (RHEL 8+ supported since v2.5.10):
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download the `PyMOL-<ver>_<build>-Linux-x86_64-py310.tar.bz2` bundle,
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unpack, run `./pymol`. The recipe downloads the bundle from the public
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pymol-storage GCS bucket (sha256-verified), unpacks it and moves the
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bundle contents into `$PREFIX`; the `pymol` launcher sits at the PREFIX
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root, so the modulefile does `prepend-path PATH $PREFIX` (the bundle's
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private `bin/` with its own python is deliberately NOT on PATH).
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Versions before 3.1.8 in this module's git history were open-source
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builds (git clone + setup.py) against merlin-era psi-python modules;
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see https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL
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if that route is ever needed again.
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### License file
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The bundle runs unlicensed with limited features. Site-wide: drop the
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SLM license file at `$PREFIX/share/pymol/license.lic`. Per user: PyMOL
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prompts on first start (get the file from https://pymol.org/dsc/ip/license/).
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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 pymol
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modbuild build 3.1.8
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module use MX unstable && module load pymol/3.1.8
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```
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## Verifying the install
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```sh
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which pymol # -> /opt/psi/MX/pymol/3.1.8/pymol
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pymol -cq # headless no-op: exits 0 without X
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pymol # GUI check, needs X
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```
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## Adding a new version
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Check the exact bundle filename on https://pymol.org (the `_0` build
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number and `py310` tag change between releases), update `urls:` if
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needed, add the version + tarball sha256 in `files/config.yaml`, then
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`modbuild build <version>` (modbuild/2.1.3) on a Ra login node.
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