Difference between revisions of "Fuse"

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===DESCRIPTION===
+
'''fuse''' joins two objects into one by forming a bond.  A copy of
    "fuse" joins two objects into one by forming a bond.  A copy of
+
the object containing the first atom is moved so as to form an
  the object containing the first atom is moved so as to form an
+
approximately reasonable bond with the second, and is then merged
  approximately resonable bond with the second, and is then merged
+
with the first object.
  with the first object.
 
 
   
 
   
===USAGE===
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== Usage ==
  fuse (selection1), (selection2)
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 +
fuse [ selection1 [, selection2 [, mode [, recolor [, move ]]]]]
 +
 
 +
== Arguments ==
 
   
 
   
===PYMOL API===
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* selection1 = str: single atom selection (will be copied to object 2) {default: (pk1)}
<source lang="python">
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* selection2 = str: single atom selection {default: (pk2)}
  cmd.fuse( string selection1="(pk1)", string selection2="(pk2)" )
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* mode = int: {default: 0}
  </source>
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** mode=0:
 +
** mode=1: adopt segi/chain/resn`resi
 +
** mode=2: adopt segi/chain
 +
** mode=3: don't move and don't create a bond, just combine into single object
 +
* recolor = bool: recolor C atoms to match target {default: 1}
 +
* move = bool: {default: 1}
 +
 
 +
== Example ==
 +
 
 +
Phosphorylate a serine residue:
 +
 
 +
  fetch 1ubq, async=0
 
   
 
   
===NOTES===
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fragment phosphite
  Each selection must include a single atom in each object.
+
remove phosphite & elem H
  The atoms can both be hydrogens, in which case they are
 
  eliminated, or they can both be non-hydrogens, in which
 
  case a bond is formed between the two atoms.
 
 
   
 
   
===SEE ALSO===
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fuse phosphite & elem P, /1ubq///65/OG, mode=1
 +
delete phosphite
 +
 +
show sticks, resi 65
 +
orient resi 65
 +
unpick
 +
 
 +
== Notes ==
 +
 
 +
Each selection must include a single atom in each object.
 +
The atoms can both be hydrogens, in which case they are
 +
eliminated, or they can both be non-hydrogens, in which
 +
case a bond is formed between the two atoms.
 +
 
 +
== See Also ==
  
  [[Cmd bond]], [[Cmd unbond]], [[Cmd attach]], [[Cmd replace]], [Cmd fuse]], [[Cmd remove_picked]]  
+
[[Bond]], [[Unbond]], [[Attach]], [[Replace]], [[Remove_picked]]  
 
   
 
   
  
[[Category:Commands|fuse]]
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[[Category:Commands|Fuse]]
 +
[[Category:Editing Module|Fuse]]

Latest revision as of 19:22, 21 February 2016

fuse joins two objects into one by forming a bond. A copy of the object containing the first atom is moved so as to form an approximately reasonable bond with the second, and is then merged with the first object.

Usage

fuse [ selection1 [, selection2 [, mode [, recolor [, move ]]]]]

Arguments

  • selection1 = str: single atom selection (will be copied to object 2) {default: (pk1)}
  • selection2 = str: single atom selection {default: (pk2)}
  • mode = int: {default: 0}
    • mode=0:
    • mode=1: adopt segi/chain/resn`resi
    • mode=2: adopt segi/chain
    • mode=3: don't move and don't create a bond, just combine into single object
  • recolor = bool: recolor C atoms to match target {default: 1}
  • move = bool: {default: 1}

Example

Phosphorylate a serine residue:

fetch 1ubq, async=0

fragment phosphite
remove phosphite & elem H

fuse phosphite & elem P, /1ubq///65/OG, mode=1
delete phosphite

show sticks, resi 65
orient resi 65
unpick

Notes

Each selection must include a single atom in each object. The atoms can both be hydrogens, in which case they are eliminated, or they can both be non-hydrogens, in which case a bond is formed between the two atoms.

See Also

Bond, Unbond, Attach, Replace, Remove_picked