Jmol/Visualizing large molecules: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 7: | Line 7: | ||
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. (Files in the [[Atomic coordinate files#mmCIF_Data_Format|mmCIF format]] can be read by Jmol, and do not suffer from this limitation.) [[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. Jmol ignores the atom serial number, columns 7-11 in the PDB file, instead assigning its own ''atomIndex'' number, unique for each atom, and not redundant between models. Jmol can handle PDB files containing >100,000 atoms. | 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. (Files in the [[Atomic coordinate files#mmCIF_Data_Format|mmCIF format]] can be read by Jmol, and do not suffer from this limitation.) [[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. Jmol ignores the atom serial number, columns 7-11 in the PDB file, instead assigning its own ''atomIndex'' number, unique for each atom, and not redundant between models. Jmol can handle PDB files containing >100,000 atoms. | ||
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]]. 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. The biological unit contains 2 asymmetric units. | 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]]. | ||
====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 this command: | |||
:<tt>load http://www.protein.osaka-u.ac.jp/olabb/tsukihara/mvp/mvp_39mer.pdb filter "*.ca"</tt> | |||
===62 Chains=== | ===62 Chains=== | ||
