Alternate locations
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| - | Some [[Atomic_coordinate_file#PDB_Data_Format|PDB files]] have alternate locations (altlocs) for some atoms. Each atom that has altlocs is marked with an altloc identifier, typically A and B. | + | Some [[Atomic_coordinate_file#PDB_Data_Format|PDB files]] have alternate locations (altlocs) for some atoms. Each atom that has altlocs is marked with an altloc identifier, typically A and B. At sufficiently high [[resolution]], two positions may be visible in the [[electron density map]] for certain atoms. If these have approximately equal densities, each alternate location will be assigned an occupancy of 50%. Sometimes 3 or even more alternate locations may be distinguished (see examples in the following section). |
| + | ==Visualizing alternate locations== | ||
| + | [http://firstglance.jmol.org FirstGlance in Jmol] tells you how many atoms have alternate locations (when you are in ''more details'' mode), and the range of occupancies assigned to them. It can animate atoms with two alternate locations. Examples: | ||
| + | *These links display the model in FirstGlance. Look in the | ||
| + | [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab] for ''alternate locations''. | ||
| + | * | ||
| + | |||
| + | ==Models with the most alternate locations== | ||
The [http://oca.weizmann.ac.il OCA Database and Browser] highlights the structure with the most 'altlocs'. See [[Believe It or Not!]] within Proteopedia for that [[Protein Data Bank]] entry and other information mined from [[User:OCA|OCA]]. | The [http://oca.weizmann.ac.il OCA Database and Browser] highlights the structure with the most 'altlocs'. See [[Believe It or Not!]] within Proteopedia for that [[Protein Data Bank]] entry and other information mined from [[User:OCA|OCA]]. | ||
| + | |||
| + | ==PDB Format== | ||
The altloc identifier occupies the 17th column for the ATOM records section of the [http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_62.html PDB format]. | The altloc identifier occupies the 17th column for the ATOM records section of the [http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_62.html PDB format]. | ||
| - | == | + | ==CIF Format== |
| - | + | In the [http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html mmCIF format correspondence] may be 'alt_id'. However, because that is listed as corresponding to 'alt_loc' , it is unclear if that is the same as 'altLoc' listed in the [http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_62.html PDB format guide]. | |
==See Also== | ==See Also== | ||
Revision as of 19:41, 27 April 2021
Some PDB files have alternate locations (altlocs) for some atoms. Each atom that has altlocs is marked with an altloc identifier, typically A and B. At sufficiently high resolution, two positions may be visible in the electron density map for certain atoms. If these have approximately equal densities, each alternate location will be assigned an occupancy of 50%. Sometimes 3 or even more alternate locations may be distinguished (see examples in the following section).
Contents |
Visualizing alternate locations
FirstGlance in Jmol tells you how many atoms have alternate locations (when you are in more details mode), and the range of occupancies assigned to them. It can animate atoms with two alternate locations. Examples:
- These links display the model in FirstGlance. Look in the
Molecule Information Tab for alternate locations.
Models with the most alternate locations
The OCA Database and Browser highlights the structure with the most 'altlocs'. See Believe It or Not! within Proteopedia for that Protein Data Bank entry and other information mined from OCA.
PDB Format
The altloc identifier occupies the 17th column for the ATOM records section of the PDB format.
CIF Format
In the mmCIF format correspondence may be 'alt_id'. However, because that is listed as corresponding to 'alt_loc' , it is unclear if that is the same as 'altLoc' listed in the PDB format guide.
