Retain order: Difference between revisions
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= | The [[retain_order]] setting keeps atoms in the original order, instead of [[sort|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. | ||
set | 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 [http://viperdb.scripps.edu/ 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 == | == Syntax == | ||
| Line 7: | Line 12: | ||
<source lang="python"> | <source lang="python"> | ||
set retain_order,[0,1] | set retain_order,[0,1] | ||
</source> | </source> | ||
| Line 14: | Line 18: | ||
Original PDB: | Original PDB: | ||
<source> | <source lang="diff"> | ||
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 | 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 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 | ||
| Line 24: | Line 28: | ||
Loaded and exported with retain_order set to 0 | Loaded and exported with retain_order set to 0 | ||
<source> | <source lang="diff"> | ||
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C | 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 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O | ||
| Line 33: | Line 37: | ||
</source> | </source> | ||
Loaded and exported with retain_order set to 1 | Loaded and exported with retain_order set to 1 | ||
<source> | <source lang="diff"> | ||
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C | 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 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H | ||
| Line 41: | Line 45: | ||
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O | ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O | ||
</source> | </source> | ||
== See Also == | |||
* [[sort]] | |||
* [[pdb_hetatm_sort]] | |||
* [[pdb_insertions_go_first]] | |||
* [[pdb_retain_ids]] | |||
* [[alter]] (can modify '''rank''') | |||
[[Category:Settings|Retain Order]] | [[Category:Settings|Retain Order]] | ||
Latest revision as of 09:48, 2 March 2017
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)