Jmol/Visualizing large molecules: Difference between revisions
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This limitation requires that models containing >=100,000 atoms be split into two or more PDB files, or else represented as artificially separated models in a single PDB file. These work-arounds are awkward for visualization. An example is the combination of portions of the two files [[1jgo]] and [[1giy]] for visualization of a complete [[Ribosome]]. | This limitation requires that models containing >=100,000 atoms be split into two or more PDB files, or else represented as artificially separated models in a single PDB file. These work-arounds are awkward for visualization. An example is the combination of portions of the two files [[1jgo]] and [[1giy]] for visualization of a complete [[Ribosome]]. | ||
<table border=0 align="right" style="background:black;"><tr><td> | <table border=0 align="right" style="background:black; text:white;"><tr><td> | ||
[[Image:RatLiverVault2.png]] | [[Image:RatLiverVault2.png]] | ||
</td><td> | </td><td> | ||
[[Image:RatLiverVault1.png]] | [[Image:RatLiverVault1.png]] | ||
</td></tr><tr><td colspan="2"> | </td></tr><tr><td colspan="2"><center> | ||
Rat Liver Vault, alpha carbon atoms only. | Rat Liver Vault, alpha carbon atoms only. | ||
</td></tr></table> | </center></td></tr></table> | ||
====241,956 Atoms: Rat Liver Vault==== | ====241,956 Atoms: Rat Liver Vault==== | ||
The rat liver vault needed to be split into 3 PDB files: [[2zuo]], [[2zv4]], and [[2zv5]]. Each file contains 80,652 atoms in 13 chains, for a total in the asymmetric unit of 241,956 atoms in 39 chains (A-Z, a-m). The biological unit contains 2 asymmetric units. Fortunately, the authors provide [http://www.protein.osaka-u.ac.jp/olabb/tsukihara/mvp/index.html PDB files containing complete asymmetric units]. However, these are 18 megabyte files, and do not fit in Jmol/java default memory. The methods [#|below] will enable you to visualize an asymmetric unit as alpha carbon atoms only, for example with these commands (the load command will take about a full minute): | The rat liver vault needed to be split into 3 PDB files: [[2zuo]], [[2zv4]], and [[2zv5]]. Each file contains 80,652 atoms in 13 chains, for a total in the asymmetric unit of 241,956 atoms in 39 chains (A-Z, a-m). The biological unit contains 2 asymmetric units. Fortunately, the authors provide [http://www.protein.osaka-u.ac.jp/olabb/tsukihara/mvp/index.html PDB files containing complete asymmetric units]. However, these are 18 megabyte files, and do not fit in Jmol/java default memory. The methods [#|below] will enable you to visualize an asymmetric unit as alpha carbon atoms only, for example with these commands (the load command will take about a full minute): | ||
