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. 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 [http://wiki.jmol.org/index.php/Jmol_Applet#Giving_JmolApplet_more_memory_to_work_with allocated more than the default amount of memory to java] on your computer). | 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 [http://wiki.jmol.org/index.php/Jmol_Applet#Giving_JmolApplet_more_memory_to_work_with 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. | ||
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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. | 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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