Jmol/Visualizing large molecules

Some molecular models ("molecules") are so large that they will not fit within the default amount of computer memory allocated to Jmol (which is the default amount of memory allocated to java). While it is possible to increase the memory allocated to java, most users will not do this, and hence, will not be able to display, in Proteopedia or Jmol, molecules that exceed a certain size.

Maximum Size Per ModelMaximum Size Per Model

Strictly speaking, the format of PDB files is limited to 99,999 atoms in a single model, because there are only 5 columns allocated to atom serial numbers. 3cc2 is a model of a large ribosomal subunit containing 99,049 atoms (close to the limit for a single PDB file). Most likely it will display in Jmol when you go to that page. Jmol ignores the atom serial number in the PDB file, and can handle PDB files containing >100,000 atoms.

Multiple Model FilesMultiple Model Files

The largest PDB files in the Protein Data Bank are those containing multiple models of large molecules. Since the atom serial numbers start at 1 in each model, these can get very large. An example is 3ezb, which contains 40 models (determined by solution NMR). Each model contains 5,323 atoms (including 2,694 hydrogen atoms); the 40 model file contains 212,920 atoms, and the PDB file is 16.5 megabytes in size. When you visit the page 3ezb, the ensemble will fail to display, producing an "out of memory" error (unless you have allocated more than the default amount of memory to java on your computer). There are files in the PDB several-fold larger than 3ezb. For example, 2hyn is a 64 megabyte file containing 826,896 atoms in 184 models.

Biological AssembliesBiological Assemblies

However, biological unit assemblies generated from PDB files often exceed this limit by using redundant serial numbers for copied chains. Luckily, Jmol ignores the serial numbers in the PDB file, and can handle models with >100,000 atoms.