Difference between revisions of "Flag"
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[[Flag]] is a command to set or clear ''flags'' on atom sets. A flag is just some atom-specific property. A flag is either on or off for a residue. Possible flags are: | [[Flag]] is a command to set or clear ''flags'' on atom sets. A flag is just some atom-specific property. A flag is either on or off for a residue. Possible flags are: | ||
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− | = Examples = | + | {| class="wikitable" |
+ | |- | ||
+ | ! Flag name | ||
+ | ! Value | ||
+ | ! Description | ||
+ | ! Notes | ||
+ | |- | ||
+ | | '''focus''' | ||
+ | | 0 | ||
+ | | Atoms of Interest (i.e. a ligand in an active site) | ||
+ | |rowspan="6"| Reserved for molecular modeling. | ||
+ | |||
+ | Affects [[Molecular Sculpting|sculpting]]. | ||
+ | |- | ||
+ | | '''free''' | ||
+ | | 1 | ||
+ | | Free Atoms (free to move subject to a force-field) | ||
+ | |- | ||
+ | | '''restrain''' | ||
+ | | 2 | ||
+ | | Restrained Atoms (typically harmonically constrained) | ||
+ | |- | ||
+ | | '''fix''' | ||
+ | | 3 | ||
+ | | Fixed Atoms (no movement allowed) | ||
+ | |- | ||
+ | | '''exclude''' | ||
+ | | 4 | ||
+ | | Atoms which should not be part of any simulation | ||
+ | |- | ||
+ | | '''study''' | ||
+ | | 5 | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | 6 | ||
+ | | Protein (<code>polymer.protein</code> selector) | ||
+ | |rowspan="2"| See [[auto_classify_atoms]] and [[auto_show_classified]] | ||
+ | |- | ||
+ | | | ||
+ | | 7 | ||
+ | | Nucleic acid (<code>polymer.nucleic</code> selector) | ||
+ | |- | ||
+ | | | ||
+ | | 8-15 | ||
+ | | ''Free for end users to manipulate'' | ||
+ | |rowspan="2"| | ||
+ | |- | ||
+ | | | ||
+ | | 16-23 | ||
+ | | Reserved for external GUIs and linked applications | ||
+ | |- | ||
+ | | '''exfoliate''' | ||
+ | | 24 | ||
+ | | '''Deprecated'''. Remove surface from atoms when surfacing. Redundant with excluding those atoms from the selection in <code>show surface, sele</code> | ||
+ | |rowspan="2"| Affects [[surface]] (with [[surface_mode]]=0), [[dots]] (with [[trim_dots]]=on), [[Get_Area|get_area]] | ||
+ | |- | ||
+ | | '''ignore''' | ||
+ | | 25 | ||
+ | | Ignore atoms altogether when surfacing | ||
+ | |- | ||
+ | | '''no_smooth''' | ||
+ | | 26 | ||
+ | | Do not smooth atom position | ||
+ | |rowspan="1"| Affects [[cartoon]] | ||
+ | |- | ||
+ | | | ||
+ | | 27 | ||
+ | | Polymer | ||
+ | |rowspan="5"| See [[auto_classify_atoms]] and [[auto_show_classified]] | ||
+ | |||
+ | See [[Selection Algebra]] "Chemical classes" | ||
+ | |- | ||
+ | | | ||
+ | | 28 | ||
+ | | Solvent | ||
+ | |- | ||
+ | | | ||
+ | | 29 | ||
+ | | Organic | ||
+ | |- | ||
+ | | | ||
+ | | 30 | ||
+ | | Inorganic | ||
+ | |- | ||
+ | | | ||
+ | | 31 | ||
+ | | Guide atom (e.g. CA in proteins) | ||
+ | |} | ||
+ | |||
+ | == Usage == | ||
+ | |||
+ | flag flag, selection [, action [, quiet ]] | ||
+ | |||
+ | If the [[auto_indicate_flags]] setting is true, then PyMOL will automatically create a selection called "indicate" which contains all atoms with that flag after applying the command. | ||
+ | |||
+ | == Arguments == | ||
+ | |||
+ | * '''flag''' = int or str: Flag name or value | ||
+ | * '''selection''' = str: atom selection | ||
+ | * '''action''' = set|clear|reset: ''Note that "reset" will set the flag on the given selection, and clear it on all other atoms'' {default: reset} | ||
+ | |||
+ | == Examples == | ||
+ | |||
+ | [[File:flags-ignore-exfoliate.png|thumb|right|CYS residue with flag "ignore" (left) and flag "exfoliate" (right)]] | ||
+ | |||
+ | <syntaxhighlight lang="python"> | ||
+ | fab AC | ||
+ | |||
+ | # Image on the left | ||
+ | flag ignore, resn CYS | ||
+ | show surface | ||
+ | |||
+ | # Image on the right | ||
+ | flag ignore, all, clear | ||
+ | flag exfoliate, resn CYS | ||
+ | rebuild surface | ||
+ | </syntaxhighlight> | ||
+ | |||
<source lang="python"> | <source lang="python"> | ||
− | # | + | # in sculpting, ensure the newMethyl group just added doesn't move around |
− | + | flag fix, newMethyl | |
− | + | ||
− | flag | + | # Introspect the flags bitmask |
− | # | + | iterate all, print(hex(flags)) |
− | |||
− | # | + | # Select atoms with "fix" flag |
− | + | select fixedatoms, flag 3 | |
− | flag | ||
</source> | </source> | ||
[[Category:Commands]] | [[Category:Commands]] |
Latest revision as of 04:44, 6 August 2020
Flag is a command to set or clear flags on atom sets. A flag is just some atom-specific property. A flag is either on or off for a residue. Possible flags are:
Flag name | Value | Description | Notes |
---|---|---|---|
focus | 0 | Atoms of Interest (i.e. a ligand in an active site) | Reserved for molecular modeling.
Affects sculpting. |
free | 1 | Free Atoms (free to move subject to a force-field) | |
restrain | 2 | Restrained Atoms (typically harmonically constrained) | |
fix | 3 | Fixed Atoms (no movement allowed) | |
exclude | 4 | Atoms which should not be part of any simulation | |
study | 5 | ||
6 | Protein (polymer.protein selector)
|
See auto_classify_atoms and auto_show_classified | |
7 | Nucleic acid (polymer.nucleic selector)
| ||
8-15 | Free for end users to manipulate | ||
16-23 | Reserved for external GUIs and linked applications | ||
exfoliate | 24 | Deprecated. Remove surface from atoms when surfacing. Redundant with excluding those atoms from the selection in show surface, sele
|
Affects surface (with surface_mode=0), dots (with trim_dots=on), get_area |
ignore | 25 | Ignore atoms altogether when surfacing | |
no_smooth | 26 | Do not smooth atom position | Affects cartoon |
27 | Polymer | See auto_classify_atoms and auto_show_classified
See Selection Algebra "Chemical classes" | |
28 | Solvent | ||
29 | Organic | ||
30 | Inorganic | ||
31 | Guide atom (e.g. CA in proteins) |
Usage
flag flag, selection [, action [, quiet ]]
If the auto_indicate_flags setting is true, then PyMOL will automatically create a selection called "indicate" which contains all atoms with that flag after applying the command.
Arguments
- flag = int or str: Flag name or value
- selection = str: atom selection
- action = set|clear|reset: Note that "reset" will set the flag on the given selection, and clear it on all other atoms {default: reset}
Examples
fab AC
# Image on the left
flag ignore, resn CYS
show surface
# Image on the right
flag ignore, all, clear
flag exfoliate, resn CYS
rebuild surface
# in sculpting, ensure the newMethyl group just added doesn't move around
flag fix, newMethyl
# Introspect the flags bitmask
iterate all, print(hex(flags))
# Select atoms with "fix" flag
select fixedatoms, flag 3