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° | Oligomerize<Obj|All> | - |
Oligomerize objects to generate the biologically active form |
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| | | Command | | Argument |
| Datatype | | Default | | Min | | Max | |
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| Format: | | Oligomerize<Obj|All> | Object selection, | |
SELECTION | | - | | - |
| - | | |
| | Center = Yes | No | | STRING | | Yes |
| - | | - | | |||
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| Python: | | resultlist = Oligomerize<Obj|All>(selection1,center=None) | | ||||||||||
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| Menu: | | Edit > Oligomerize | | ||||||||||
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| Related: | | Duplicate , Crystallize |
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| Required: | |
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The Oligomerize command creates the biologically relevant oligomer of the selected object.
To save space, many PDB files contain only a single monomer even though a larger oligomer has been crystallized. These PDB files then specify the transformations required to create the complete olgomer in a special remark named
'REMARK 350'. This remark with the contained BIOMT transformations is interpreted by the
Oligomerize command.
If REMARK 350 is not present in your PDB file, Oligomerize
cannot help, and the only remaining option is to check the PQS database at
http://pqs.ebi.ac.uk.
Example 1:
OligomerizeObj 3
Create the biologically relevant oligomer of object 3 using REMARK
350 in the PDB file and center the new object.
Example 2:
OligomerizeAll Center=No
Oligomerize all objects but do not center afterwards.
Example 3:
objlist() = OligomerizeObj 5
Oligomerize object 5 and assign the numbers of the objects
(including the initially selected one) to 'objlist'.
Example macro:
# EXAMPLE Oligomerize # Requires YASARA Model Clear LoadPDB 3crx OligomerizeObj 3crx Pos 0,0,128 Ori 17,91,0 Style Tube SecStrPar TubeRadius=0.19 ColorMol Protein,Blue,Cyan ShowAtom NucAcid SideChain StickRadius 100
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| Figure: Result of the example macro above. |