GemmiMol is a web-based macromolecular viewer focused on electron density. It is a successor of the deprecated UglyMol.

It makes models and e.den. maps easy to recognize, navigate and interpret –: for crystallographers. It looks like Coot and walks (mouse controls) like Coot. But it’s only a viewer. For situations when you want a quick look and simple edits without downloading the data and starting Coot. For instance, when screening Dimple results in a synchrotron. Of course, for this to work, it needs to be integrated into a website that provides the data access (see the UglyMol FAQ on how to do it). See also the integration page for notes, including how to provide monomer CIF files.

Try it:

• 1MRU (60kDa, 3Å), and in dual view with PDB_REDO,
• 3KW8 (30kDa, 2.3Å),
• 4UN4 (protein-DNA complex, 2.37Å),
• a blob (Dimple result, thaumatin, 1.4Å),
• or any local file or wwPDB entry.

Small molecule from COD: caffeine (COD 1542540).

It also has a reciprocal space spin-off.

GemmiMol is a small (~3 KLOC) project (see changelog). The plan is to keep it small. But if you’re missing some functionality, it won’t hurt if you get in touch – use Issues or email.

See the UglyMol Wiki for more information.

current version:
GemmiMol 0.8.8 (0.8.8)
Gemmi v0.7.5-152-g4bf01c29

Integration notes: integration