Jmol/Visualizing large molecules: Difference between revisions
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==Multiple Model Files== | ==Multiple 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 files can get very large (>1,000,000 atoms is possible). 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. | 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 files can get very large (>1,000,000 atoms is possible). 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. | ||
