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. | ||
Strictly speaking, the format of [[PDB files]] is limited to 99,999 atoms in a single model, because there are only 5 columns allocated to atom serial numbers. | Strictly speaking, the format of [[PDB files]] is limited to 99,999 atoms in a single model, because there are only 5 columns allocated to atom serial numbers. [[3cc2]] is a model of a large ribosomal subunit containing 99,049 atoms (close to the limit for a single PDB file). Most likely it will display in Jmol when you go to that page. | ||
[[ | 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. | ||
Revision as of 02:25, 1 January 2011
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 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.
Strictly speaking, the format of PDB files is limited to 99,999 atoms in a single model, because there are only 5 columns allocated to atom serial numbers. 3cc2 is a model of a large ribosomal subunit containing 99,049 atoms (close to the limit for a single PDB file). Most likely it will display in Jmol when you go to that page.
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.