Jmol/Visualizing large molecules: Difference between revisions
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Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
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:<tt>zap | :<tt>zap | ||
:load models {1 1 1} =2hyn</tt> | :load models {1 1 1} =2hyn</tt> | ||
:In less than 30 seconds, the first model from the ensemble in 2hyn should appear in Jmol. | |||
*'''Save The First Model''': Type this command: | |||
:<tt>write pdb 2hyn_model1.pdb</tt> | |||
:Now you should find a new file 2hyn_model1.pdb in your working folder. You can load it with this command: | |||
:<tt>load 2hyn_model1.pdb</tt> | |||
:You can also upload it to Proteopedia for use in molecular scenes generated with Proteopedia's [[SAT]]. | |||
==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. | ||
