WeMOL · Browser-based molecular viewer (based on PyMOL (TM) technology)

Rendering …

Starting the molecular viewer …

The first visit downloads the Python / PyMOL WebAssembly package (about 10 MB). Your browser caches it afterwards, so later visits start much faster. Please wait.

PyMOL>

Files generated in the browser

PyMOL commands such as save / png write into an in-memory file system inside this browser tab — they do not appear on your local disk by themselves. When a command finishes, the page downloads the generated files for you automatically; use this list to download or delete them again at any time. These files are lost when the page is reloaded.

Display

Background color

Internal GUI

Common commands

Type PyMOL commands into the console below; prefix a line with / to run it as Python code instead:

fetch 1ubq
show cartoon
spectrum chain
/print(cmd.get_names())

Saving files

save myfile.pse writes into the browser's in-memory file system: when the command finishes the page downloads the file automatically, and you can re-download or delete it from the Files tab. Everything is gone after a reload — keep important results on your own disk.

save myfile.pse
save out.pdb, all, format=pdb
/pymol.cmd.save("out.mol2", "all")

Performance tips

Surfaces and ray tracing are slow in a browser; for large structures start with the cartoon representation. On mobile, ?scale=1 lowers the rendering resolution.

Mouse / touch

Left drag rotate
Middle drag or Ctrl + left drag pan
Right drag / wheel zoom
Right click open the atom menu

Files

Drag a structure file onto the canvas, or click “Open file”. PDB / mmCIF / MOL2 / SDF / XYZ / PSE and more are supported, and .gz archives are decompressed automatically.

Performance mode

By default Pyodide + WebGL run in a Web Worker (OffscreenCanvas), so the page stays responsive while ray tracing or generating surfaces. For compatibility checks, ?worker=0 switches back to main-thread rendering; ?timings prints startup timings.

Saving files

PyMOL's save myfile.pse writes into the browser's in-memory file system; when the command finishes the page downloads the result automatically. The Files tab can also download or delete these files. They are lost on reload.

About

WeMOL is a WebAssembly port of the open-source PyMOL (TM): the C++ rendering core is compiled directly to wasm, Emscripten creates the WebGL context, and the Python layer runs on Pyodide. Everything is computed locally in your browser — your structure data is never uploaded.

WeMOL is a derivative work containing PyMOL source code. Its name and branding are WeMOL so that it is plainly distinguished from the PyMOL products distributed by Schrödinger, LLC; it is not affiliated with, or endorsed by, Schrödinger, LLC.

License & Trademark

This viewer uses the open-source PyMOL source code and is distributed under its license terms. The original copyright notice, license terms and trademark notice follow, unmodified:

Open-Source PyMOL Copyright Notice

The Open-Source PyMOL source code is copyrighted, but you can freely use and
copy it as long as you don't change or remove any of the Copyright notices.
The Open-Source PyMOL product is made available under the following open-source
license terms:

Open-Source PyMOL is Copyright (C) Schrodinger, LLC.  All Rights Reserved

Permission to use, copy, modify, distribute, and distribute modified versions of
this software and its built-in documentation for any purpose and without fee is
hereby granted, provided that the above copyright notice appears in all copies
and that both the copyright notice and this permission notice appear in
supporting documentation, and that the name of Schrodinger, LLC not be used in
advertising or publicity pertaining to distribution of the software without
specific, written prior permission.

SCHRODINGER, LLC DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING
ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL
SCHRODINGER, LLC BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR
ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

PyMOL Trademark Notice

PyMOL (TM) is a trademark of Schrodinger, LLC. Derivative software which contains
PyMOL source code must be plainly distinguished from any and all PyMOL products
distributed by Schrodinger, LLC in all publicity, advertising, and documentation.

The slogans, "Includes PyMOL (TM).", "Based on PyMOL (TM) technology.",
"Contains PyMOL (TM) source code.", and "Built using PyMOL (TM).", may be used in
advertising, publicity, and documentation of derivative software provided that
the notice, "PyMOL is a trademark of Schrodinger, LLC.", is included in a
footnote or at the end of the document.

All other endorsements employing the PyMOL trademark require specific, written
prior permission.

Full source code and license details: schrodinger/pymol-open-source · pymol.org