# 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

```sh
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

```sh
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.