Which molecule viewer to open

The short answer

Three of themcover almost everything

There are dozens of them. Almost all real work happens in PyMOL, VMD or ChimeraX, and the choice is not close once you know the task.

PyMOL

The one figures are made in. Strong ray tracer, scriptable in Python, and everyone can read its commands.

VMD

Built for trajectories. Handles very large systems and has analysis built in, at the cost of a hard interface.

ChimeraX

The modern one. Best with maps and structures together, and much the friendliest of the three to learn.

Pick by the task

What are youactually doing

Nobody needs the best viewer. They need the one that is good at the specific thing in front of them.

A figure for a paperPyMOL. Ray-traced output, fine control over representation, and a script you can rerun later.

Watching a trajectoryVMD. Written for exactly this, reads GROMACS and AMBER formats, and does not choke on long runs.

Density maps, or big assembliesChimeraX. Cryo-EM maps, fitting and very large complexes are where it clearly leads the others.

Building or editing a moleculeAvogadro. A real editor rather than a viewer, with geometry cleanup that behaves sensibly.

Showing someone quicklyMolView or Mol* in a browser. Nothing to install, and good enough to settle a conversation.

The rest

Still worthknowing about

Not every job is a production figure or a million-atom trajectory, and some of these are better for what they are for.

Jmol

Java, open source, and still the easiest thing to embed in teaching material.

RasMol

Ancient and tiny. You will meet it in old papers and old scripts rather than choose it.

Marvin, Discovery Studio

Chemistry-first and commercial. Strong for drawing and cheminformatics, licensed accordingly.

A note on what these are not: GROMACS, AMBER and LAMMPS are simulation engines, not viewers. They ship analysis tools and write trajectories, but you will open the result in something on this page. Keeping that distinction clear saves a surprising amount of confusion when reading tutorials.

Running one

A window,or no window at all

Most of these expect a display. On a rented machine you have two honest options, and the second is usually better.

In a tabWith a desktopa full session on the machine

A scriptHeadlessrender offscreen, write PNGs

Stop itThenthe images are all you needed

Either run the viewer with a desktop on the machine and work in it directly, or drive it headless from a script and bring back images. The second scales: PyMOL and ChimeraX both take a command file, render offscreen, and write PNGs. For a hundred frames or a hundred structures, that is the only sane route, and it means the machine can be stopped the moment the images are written.

On a machine

PyMOL isalready built

Nothing here needs compiling. Pick a machine, and these two commands put it on there.

hub://pymol

$ dxflow workflow create --identity pymol hub://pymol

$ dxflow workflow start pymol

Start a machine What PyMOL needs

Read it, then run itPrepaid and by the hour, on a machine that is yours about a minute after you ask.

Start a machine All notes