Jmol/Visualizing large molecules: Difference between revisions
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With large multiple-chain assemblies, or multiple-model ensembles, typically you want to see only the backbone traces. Backbone traces can be visualized from only the alpha carbon atoms (or for nucleic acids, the phosphorus atoms). Jmol can extract ("filter") specified atoms from the PDB file, thereby saving memory. For example, 2hyn contains 4,494 atoms/model (half of which are hydrogen atoms), and 184 models, totalling 826,896 atoms. There are 260 alpha carbon atoms/model, or a total of 47,840 atoms. The alpha carbons represent less than 6% of the original atoms, or a nearly 20-fold reduction in memory requirements. | With large multiple-chain assemblies, or multiple-model ensembles, typically you want to see only the backbone traces. Backbone traces can be visualized from only the alpha carbon atoms (or for nucleic acids, the phosphorus atoms). Jmol can extract ("filter") specified atoms from the PDB file, thereby saving memory. For example, 2hyn contains 4,494 atoms/model (half of which are hydrogen atoms), and 184 models, totalling 826,896 atoms. There are 260 alpha carbon atoms/model, or a total of 47,840 atoms. The alpha carbons represent less than 6% of the original atoms, or a nearly 20-fold reduction in memory requirements. | ||
Using the Jmol application from your working folder (see instructions | Using the '''Jmol application''' from your working folder (see [[Jmol/Application|'''instructions''']]), enter this command: | ||
:load =2hyn filter "*.ca" | :load =2hyn filter "*.ca" | ||
"*.ca" means "all carbon alpha atoms". After about a full minute (depending on the speed of your Internet connection), a backbone trace of the first model will appear, which means that loading and filtering are complete. These commands will display the backbone traces for all 184 models: | "*.ca" means "all carbon alpha atoms". After about a full minute (depending on the speed of your Internet connection), a backbone trace of the first model will appear, which means that loading and filtering are complete. These commands will display the backbone traces for all 184 models: | ||
