Large PDB Files: Results in FirstGlance in Jmol
Results with Jmol 10.00.46

PDB File | Molecule | Atoms | Groups | Megabytes | Models | Results in FGiJ (Jmol) | Results in Protein Explorer (MDL Chime)
1FFK | ribosome | 64K | 6.5K | 5.5 | 1 | OK |
1ZLL | phospholamban pentamer | 90K | 5.2K | 7.3 | 20 NMR | OK |
1JJ2 | ribosome | 98K | 14.7K | 8.4 | 1 | OK |
3EZB | phosphotransfer enzyme complex | 213K | 14K | 17 | 40 NMR | Fails* | Displayed OK in 50 seconds. (Including data download time)
1HTQ | glutamine synthetase | 979K | 178K | 81 | 10 XRC | Fails* | Displayed OK in 4.25 minutes. (Including data download time)

Conclusion: Jmol will load the vast majority of published PDB files. As of October, 2005, there were only about 30 files in the PDB that are larger than 1JJ2 (information thanks to Jaime Prilusky, Bioinformatics and Biological Computing, Weizmann Inst., Rehovot, Israel). Since the PDB contains >30,000 entries, <0.1 % are too large for Jmol.

* Fails: Jmol rectangle turns blank white (no "Jmol" frank), and remains blank for >5 minutes after network activity stopped. Testing was in Windows XP SP1, 3 GHz, 512 megabytes of RAM.

99,999 (100K) is the maximum possible number of atoms per model in a PDB file, since only 5 columns are provided for atom serial numbers. By virtue of having 10 models, 1HTQ has nearly 10 times this many.