Group

The Group command creates or updates a "group" object. The grouped objects are collected underneath a + sign in the object tree (see images) in the Pymol Internal Gui.

Group is tremendously helpful with multi-state or multi-structure sessions. Wildcards work great, for example:

# put all of objState into the group "ensemble".
group ensemble, objState*

• 

  Three EF-Hand proteins loaded into PyMOL

• 

  Applied the group command to the proteins via: "group efHand, *"

• 

  The plus was clicked and expanded to show the hierarchy of objects.

Usage

group name, members, action

Actions:

• add - Add member to group
• remove - Remove members from group
• open - Open the group in the panel so objects can be dragged in
• close - Close the group in the panel so nothing can be dragged in
• toggle - Switch between open or close based on current state
• auto - (Deprecated)
• ungroup - (Deprecated) use the ungroup command instead
• empty - Move members to top level but do not delete groups
• purge - Delete members but do not delete groups
• excise - Delete groups but do not delete members
• raise - (Incentive 3.1+ only) Move the specified group to the top level, relevant for groups within groups

Examples

Creating, opening and closing

group efHand, 1cll 1ggz 1sra

# allow addition and removal from the group
# If a group is open, objects can be added to or removed from 
# it by right-click+drag from the control panel
group efHand, open
# disallow addition/removal from the group
group efHand, close

More advanced usage of groups and naming

# names with dots are treated special

set group_auto_mode, 2

# load the example protein

load $TUT/1hpv.pdb, 1hpv.other

# create the new entry called ".protein" in group 1hpv

extract 1hpv.protein, 1hpv.other and polymer

# create ".ligand in the 1hpv group

extract 1hpv.ligand, 1hpv.other and organic

# supports wildcards

show sticks, *.ligand

hide lines, *.protein

show surface, *.protein within 6 of *.ligand

show lines, byres *.protein within 4 of *.ligand

set two_sided_lighting

set transparency, 0.5

set surface_color, white

# Also, to lexicographically sort the names in the control panel:

order *, yes

Notes

Group objects can usually be used as arguments to commands. It can be processed as a group or as a selection, in which case all the atoms from all objects in the group will be used.

See Also

ungroup order select