Silent install command for PyMOL 3.1.8

The exact silent switches the PyMOL installer accepts, plus a one-line command you can paste into a script, Intune Win32 app, or Configuration Manager package.

One-line silent install (x64, user scope)

PyMOL-3.1.8-Windows-x86_64.exe /S /InstallationType=JustMe

Run from the directory containing PyMOL-3.1.8-Windows-x86_64.exe. Download the installer from the Direct link below first.

Architecture	Scope	Type	Silent switches	Source
x64	user	EXE NSIS	Custom: /InstallationType=JustMe	Default for NSIS (Nullsoft)
x64	machine	EXE NSIS	Custom: /InstallationType=AllUsers	Default for NSIS (Nullsoft)

Declared by publisher means the switches come straight from the winget manifest the publisher (or community maintainer) submitted to microsoft/winget-pkgs.
Default for {type} means the manifest doesn't specify silent switches, so the framework's standard switches are shown (e.g. /S for NSIS, /quiet /norestart for MSI).

Frequently asked questions

What is the silent install command for PyMOL?

PyMOL uses EXE (NSIS). After downloading the installer, run: PyMOL-3.1.8-Windows-x86_64.exe /S /InstallationType=JustMe. The silent install switches are /S.

How do I deploy PyMOL via Intune or Configuration Manager?

Use winget for the cleanest path: winget install --id Schrodinger.PyMOL --exact 3.1.8 --silent --accept-package-agreements --accept-source-agreements. If winget isn't viable in your environment, package the publisher's installer directly using the silent switches above.

Prefer the winget route? See the full PyMOL install page.