Jmol/Visualizing large molecules: Difference between revisions
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:<tt>load 2hyn_model1.pdb</tt> | :<tt>load 2hyn_model1.pdb</tt> | ||
:You can also upload it to Proteopedia for use in molecular scenes generated with Proteopedia's [[SAT]]. | :You can also upload it to Proteopedia for use in molecular scenes generated with Proteopedia's [[SAT]]. | ||
===Displaying Only Alpha Carbon Atoms=== | |||
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 specified atoms from the PDB file, thereby saving memory. For example, 2hyn contains 4,494 atoms/model (half of which are hydrogen atoms), and | |||
==Biological Assemblies== | ==Biological Assemblies== | ||
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. | ||
