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><tr><td> | |||
Image:RatLiverVault2.png | |||
</td><td> | |||
Image:RatLiverVault1.png | |||
</td></tr><tr><td colspan="2"> | |||
Rat Liver Vault, alpha carbon atoms only. | |||
</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 | 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): | ||
:<tt>load <nowiki>http://www.protein.osaka-u.ac.jp/olabb/tsukihara/mvp/mvp_39mer.pdb</nowiki> filter "*.ca"</tt> | :<tt>load <nowiki>http://www.protein.osaka-u.ac.jp/olabb/tsukihara/mvp/mvp_39mer.pdb</nowiki> filter "*.ca" | ||
:color chain</tt> | |||
===62 Chains=== | ===62 Chains=== | ||
