Retain order
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The retain_order setting keeps atoms in the original order, instead of sorting them by atom identifiers. The "original order" is defined by the rank property, so technically with retain_order=on, PyMOL performs a rank-assisted sort.
Setting retain_order on or off triggers resorting of atoms.
File Format Specifics
- vdb: Since PyMOL 1.8.6, retain_order is automatically set for VIPERdb files, because they don't have unique chain identifiers
- cif: When retain_order=on, then PyMOL will skip loading of missing residues, because it depends on sorting
Syntax
set retain_order,[0,1]
Example
Original PDB:
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00
Loaded and exported with retain_order set to 0
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
Loaded and exported with retain_order set to 1
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
See Also
- sort
- pdb_hetatm_sort
- pdb_insertions_go_first
- pdb_retain_ids
- alter (can modify rank)