Assembly: Difference between revisions
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When loading '''mmCIF''' structure files, the [[assembly]] setting controls whether PyMOL loads the asymmetric unit (assembly="") or a biological unit (e.g. assembly="1"). Assembly identifiers in mmCIF files can be arbitrary strings, but usually are numeric and most files define at least assembly "1". | When loading '''mmCIF''' structure files, the [[assembly]] setting controls whether PyMOL loads the asymmetric unit (assembly="") or a biological unit (e.g. assembly="1"). Assembly identifiers in mmCIF files can be arbitrary strings, but usually are numeric and most files define at least assembly "1". | ||
''New in PyMOL 1 | ''New in PyMOL 1.8'' | ||
Assemblies with more than one symmetry copy are loaded as multi-state objects with [[all_states]]=on. The assemblies should be equivalent to the '''pdb1''' files which are available from the [ftp://ftp.wwpdb.org/pub/pdb/data/biounit/ PDB ftp server]. | Assemblies with more than one symmetry copy are loaded as multi-state objects with [[all_states]]=on. The assemblies should be equivalent to the '''pdb1''' files which are available from the [ftp://ftp.wwpdb.org/pub/pdb/data/biounit/ PDB ftp server]. | ||
Latest revision as of 08:27, 1 September 2016
When loading mmCIF structure files, the assembly setting controls whether PyMOL loads the asymmetric unit (assembly="") or a biological unit (e.g. assembly="1"). Assembly identifiers in mmCIF files can be arbitrary strings, but usually are numeric and most files define at least assembly "1".
New in PyMOL 1.8
Assemblies with more than one symmetry copy are loaded as multi-state objects with all_states=on. The assemblies should be equivalent to the pdb1 files which are available from the PDB ftp server.
Examples
Download the ASU and the first assembly, show them side by side.
set assembly, ""
fetch 3bw1, asu, async=0
set assembly, 1
fetch 3bw1, assembly1, async=0
set grid_mode
See Also
- all_states
- split_states
- http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx.dic/Items/_pdbx_struct_assembly.id.html
- BiologicalUnit/Quat and BiologicalUnit: scripts to parse assembly information from PDB files