Jmol/Visualizing large molecules: Difference between revisions
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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. | 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. | ||
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. One of the largest is [[2ku2]], containing nearly one million atoms. It consists of fifty models (determined by solution [[NMR]]), each of which has seven chains and nearly 26,000 atoms. | 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. | ||
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One of the largest is [[2ku2]], containing nearly one million atoms. It consists of fifty models (determined by solution [[NMR]]), each of which has seven chains and nearly 26,000 atoms. | |||
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