Jmol/Visualizing large molecules: Difference between revisions
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==Maximum Size Per Model== | ==Maximum Size Per Model== | ||
===99,999 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. | 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]]. | 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]]. | ||
===62 Chains=== | |||
In the most recent update of the PDB data format specification ([http://www.wwpdb.org/documentation/format32/sect9.html#ATOM Version 3.2, October 2008]), chain IDs (names) must be single alphanumeric characters (A-Z, a-z, 0-9). This permits a maximum of 62 chains. This limit is not much of a problem for [[asymmetric unit|asymmetric units]]. In January, 2011, there is only one PDB entry with 62 chains ([[2zkr]]), and 4 more with 55-60 chains. | |||
Jmol can automatically apply a distinct color to each chain, up to 36 chains ([http://jmol.sourceforge.net/jscolors/#Chains Jmol Colors]). | |||
==Multiple Model Files== | ==Multiple Model Files== | ||
