Alternatively the following creates a new set from a selection of atoms
NOTE BUSTER_SET newSet = { <atom_selection> }
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The <atom_selection> must be surrounded by curly brackets.
There are currently three forms for the specifications:
- original TNT syntax as used on COMBINE and CONSTANT cards, surrounded by
curly brackets. This is explained in the TNT Users
Manual Refinement Data Statements section.
It can be understood by considering these examples:
- To define a set of all atoms in the molecule with the name CA (normally alpha Carbons):
NOTE BUSTER_SET CAs = { *|*:CA }
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- To define a set of all atoms from chain P with the name CA :
NOTE BUSTER_SET CAs = { P|*:CA }
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- To define a set of all atoms in the molecule with the name CA or CB :
NOTE BUSTER_SET CAs = { *|*:CA *|*:CB }
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- To define a set of all atoms in chain A with residue number in range 1 to 23
NOTE BUSTER_SET A1to23 = { A|1 - A|23 }
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- To define a set of all atoms in chain A with residue
number in range 1 to 6 and range 9 to 12 and residue
number 18
NOTE BUSTER_SET A1to6and9to12and18 = { A|1 - A|6 A|9 - A|12 A|18 }
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- To define a set of all atoms in chain A -
note that gelly automatically defines a set 'Chain_x' for each named chain
in the PDB file:
NOTE BUSTER_SET MychainA = { A|* }
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- To define a set of the specified atoms from residue B|57:
NOTE BUSTER_SET Back57 = { B|57:CA B|57:C B|57:N B|57:O }
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In this case it would probably be easier to use the intersection operator
- see below for alternative definition of "Back57".
- To define a set containing the atoms of residue C|61 marked as from alternate conformation A (useful for occupancy refinements):
NOTE BUSTER_SET C61a = { C|61:*.A }
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- RESTYPE this selects all atoms in one of the residue types listed.
For example:
- To define a set of all atoms residue type WAT:
NOTE BUSTER_SET WATs = { RESTYPE WAT }
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- To define a set of all atoms residue type PHE, TYR or TRP:
NOTE BUSTER_SET Aromatic = { RESTYPE PHE TYR TRP }
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- ATOMTYPE this selects all atoms declared to be of the atom types listed.
For example:
- To define a set of all hydrogen atoms H:
NOTE BUSTER_SET setH = { ATOMTYPE H }
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- To define a set of all magnesiums including ionic forms:
NOTE BUSTER_SET setMG = { ATOMTYPE MG MG2+ MG+2 }
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These kinds of selections are often useful in combination with other sets.
The {}'s produce a set definition directly containing an atom selection. This
"creates a set on the fly". There are a number of examples below. As
well as being used in NOTE BUSTER_SET they can also be used directly in the
specifications of:
NOTE BUSTER_CONSTANT ,
NOTE BUSTER_COMBINE ,
NOTE BUSTER_COMBINE_RES ,
NOTE BUSTER_NCS_...
cards in place of buster set names