Jmol/Visualizing large molecules: Difference between revisions
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Some molecular models ("molecules") are so large that they will not fit within the default amount of computer memory allocated to Jmol (which is the default amount of memory allocated to java). While it is possible to [http://wiki.jmol.org/index.php/Jmol_Applet#Giving_JmolApplet_more_memory_to_work_with increase the memory allocated to java], most users will not do this, and hence, will not be able to display, in Proteopedia or Jmol, molecules that exceed a certain size. | Some molecular models ("molecules") are so large that they will not fit within the default amount of computer memory allocated to Jmol (which is the default amount of memory allocated to java). While it is possible to [http://wiki.jmol.org/index.php/Jmol_Applet#Giving_JmolApplet_more_memory_to_work_with increase the memory allocated to java], most users will not do this, and hence, will not be able to display, in Proteopedia or Jmol, molecules that exceed a certain size. | ||
===Solutions=== | |||
Below are explained various strategies for reducing the sizes of large PDB files, enabling their main features to be displayed in the default Jmol/java memory. These strategies include displaying only the backbones (alpha carbons for proteins and phosphorus atoms for nucleic acids), and displaying one, or a subset, of the models in multiple-model files. | Below are explained various strategies for reducing the sizes of large PDB files, enabling their main features to be displayed in the default Jmol/java memory. These strategies include displaying only the backbones (alpha carbons for proteins and phosphorus atoms for nucleic acids), and displaying one, or a subset, of the models in multiple-model files. | ||
