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2020-07-20T16:19:39Z

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Speleo3: table

2020-06-23T06:42:06Z

table

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2014-03-28T02:00:43Z

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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:
* Flags 0-7 are reserved for molecular modeling
'''focus''' = 0
::Atoms of Interest (i.e. a ligand in an active site)
'''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

*Flags 8-15 are free for end users to manipulate

*Flags 16-23 are reserved for external GUIs and linked applications

* Flags 24-30 are reserved for PyMOL internal usage
'''exfoliate''' = 24
::Remove surface from atoms when surfacing
'''ignore'''=25
::Ignore atoms altogether when surfacing
'''no_smooth''' = 26
::Do not smooth atom position

* Flag 31 is reserved for coverage tracking when assigning parameters, etc.

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.

=PYMOL API=
<source lang="python">
cmd.flag(int flag, string selection, string action="reset", int indicate=0)
</source>

= Examples =
<source lang="python">
# get the area of a protein-ligand complex
get_area my_complex
# ignore the ligands when doing surface area
flag ignore, organic
# compare the surface area now
get_area my_complex

# in sculpting, ensure the newMethyl group just added
# doesn't move about
flag fix, newMethyl
</source>

[[Category:Commands]]

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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:
+{| class="wikitable"
-* Flags 0-7 are reserved for molecular modeling
+|-
-'''focus''' = 0
+! Flag name
-::Atoms of Interest (i.e. a ligand in an active site)
+! Value
-'''free''' = 1
+! Description
-::Free Atoms (free to move subject to a force-field)
+! Notes
-'''restrain''' = 2
+|-
-::Restrained Atoms (typically harmonically constrained)
+| '''focus'''
-'''fix''' = 3
+| 0
-::Fixed Atoms (no movement allowed)
+| Atoms of Interest (i.e. a ligand in an active site)
-'''exclude''' = 4
+|rowspan="6"| Reserved for molecular modeling.
-::Atoms which should not be part of any simulation
+Affects [[Molecular Sculpting|sculpting]].
-*Flags 8-15 are free for end users to manipulate
+|-
+| '''free'''
-*Flags 16-23 are reserved for external GUIs and linked applications
+| 1
+| Free Atoms (free to move subject to a force-field)
-* Flags 24-30 are reserved for PyMOL internal usage
+|-
-'''exfoliate''' = 24
+| '''restrain'''
-::Remove surface from atoms when surfacing
+| 2
-'''ignore'''=25
+| Restrained Atoms (typically harmonically constrained)
-::Ignore atoms altogether when surfacing
+|-
-'''no_smooth''' = 26
+| '''fix'''
-::Do not smooth atom position
+| 3
+| Fixed Atoms (no movement allowed)
-* Flag 31 is reserved for coverage tracking when assigning parameters, etc.
+|-
+| '''exclude'''
-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.
+| 4
+| Atoms which should not be part of any simulation
-=PYMOL API=
+|-
-<source lang="python">
+| '''study'''
-cmd.flag(int flag, string selection, string action="reset", int indicate=0)
+| 5
-</source>
 <source lang="python">
-# get the area of a protein-ligand complex
+# in sculpting, ensure the newMethyl group just added doesn't move around
-get_area my_complex
+flag fix, newMethyl
-# ignore the ligands when doing surface area
-flag ignore, organic
+# Introspect the flags bitmask
-# compare the surface area now
+iterate all, print(hex(flags))
-# in sculpting, ensure the newMethyl group just added
+# Select atoms with "fix" flag
-# doesn't move about
+select fixedatoms, flag 3
 </source>
 [[Category:Commands]]

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