Difference between revisions of "Group"

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== Overview ==
+
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.
The [[Group]] command creates or updates a "group" object.  The grouped objects are collected underneath a '''+''' sign in the object tree (see images).
 
  
 
[[Group]] is tremendously helpful with multi-state or multi-structure sessions.  Wildcards work great, for example:
 
[[Group]] is tremendously helpful with multi-state or multi-structure sessions.  Wildcards work great, for example:
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</source>
 
</source>
  
== Example ==
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== Examples ==
 +
 
 +
=== Creating, opening and closing ===
 
<source lang="python">
 
<source lang="python">
 
group efHand, 1cll 1ggz 1sra
 
group efHand, 1cll 1ggz 1sra
  
 
# allow addition and removal from the group
 
# 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
 
group efHand, open
 
# disallow addition/removal from the group
 
# disallow addition/removal from the group
 
group efHand, close
 
group efHand, close
 +
</source>
 +
 +
=== More advanced usage of groups and naming ===
 +
 +
<source lang="python">
 +
# 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
 
</source>
 
</source>
  

Latest revision as of 03:17, 4 May 2017

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*

Usage

group name, members, action

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