Group

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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*

Contents

Usage

group name, members, action

Examples

Creating, opening and closing

group efHand, 1cll 1ggz 1sra
 
# allow addition and removal from the group
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

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