Jmol/Visualizing large molecules: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 17: | Line 17: | ||
</center></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 [#Displaying Only Alpha Carbon Atoms|explained below] will enable you to visualize an asymmetric unit as alpha carbon atoms only (31,668 atoms). First, [[Jmol/Application|run the Jmol application]]. Now try 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 [[#Displaying Only Alpha Carbon Atoms|explained below]] will enable you to visualize an asymmetric unit as alpha carbon atoms only (31,668 atoms). First, [[Jmol/Application|run the Jmol application]]. Now try these commands (the load command will take about a full minute): | ||
{{Clear}} | {{Clear}} | ||
:<tt>load <nowiki>http://www.protein.osaka-u.ac.jp/olabb/tsukihara/mvp/mvp_39mer.pdb</nowiki> filter "*.ca" | :<tt>load <nowiki>http://www.protein.osaka-u.ac.jp/olabb/tsukihara/mvp/mvp_39mer.pdb</nowiki> filter "*.ca" | ||
