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Parameter selection in gelly

Appendix B: Parameter selection in gelly

Copyright © 2006 Global Phasing Ltd.
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Parameter selection overview

Parameter selection means choosing which atomic parameters (XYZ, B and OCC) are held constant or combined. gelly understands normal TNT CONSTANT and COMBINE cards. However, to take advantage of the more elaborate atom selection available in gelly the NOTE BUSTER_CONSTANT or NOTE BUSTER_COMBINE cards should be used. These are explained below.

Holding parameters fixed with the NOTE BUSTER_CONSTANT card

NOTE BUSTER_CONSTANT <Parameter_code> <Set selection>
This is similar to a standard TNT CONSTANT card but uses a set definition.
<Parameter_code> code can be 'XYZ' or 'B' or 'OCC' or 'ALL'
<Set selection> is either the name of a BUSTER_SET or an atom selection in curly brackets (explanation).

For example you want to hold the positions of main chain atoms fixed. For this the dictionary defined set 'Back' can be used:
NOTE BUSTER_CONSTANT XYZ Back
or you have a ligand with a residue number of A|500. You wish to fix the occupancy of all atoms that are not in the ligand
NOTE BUSTER_SET Ligand = { A|500 }
NOTE BUSTER_SET NotLigand = \ Ligand
NOTE BUSTER_CONSTANT OCC NotLigand
The 'NotLigand' set is everything that is not in the 'Ligand' set (protein, water, cofactors .....). The complement operator: \ absolute mode is used in the definition.

Grouping parameters together with the NOTE BUSTER_COMBINE card

NOTE BUSTER_COMBINE <Parameter_code> <Set selection>
This is similar to a standard TNT COMBINE card but uses a set definition.
<Parameter_code> code can be 'XYZ' or 'B' or 'OCC' (but not 'ALL')
<Set selection> is either the name of a BUSTER_SET or an atom selection in curly brackets (explanation).

For example you have a helix from A|50 to A|65 and you wish for the backbone of this to move as a single rigid body. BUSTER_SET cards are first used with the intersect operator: & to define the selection.
NOTE BUSTER_SET Helix1 = { A|50 - A|65 }
NOTE BUSTER_SET Helix1Back = Helix1 & Back
NOTE BUSTER_COMBINE XYZ Helix1Back
Note that it is possible to define multiple rigid bodies in gelly and mix these with normal Cartesian parameters for other atoms.

As another example let us continue developing the occupancy refinement example above. It would be sensible to combine the occupancies for all atoms of the ligand. This means that the occupancy of all atoms in the ligand will be changed by the same amount during refinement. If all the occupancies start at the same value (e.g. 1.0) then in effect a single occupancy is used for all ligand atoms.
NOTE BUSTER_SET Ligand = { A|500 }
NOTE BUSTER_SET NotLigand = \ Ligand
NOTE BUSTER_CONSTANT OCC NotLigand
NOTE BUSTER_COMBINE OCC Ligand
NOTE BUSTER_COMBINE B Ligand
The last line also combines the temperature factors for the ligand. If these all start at the same value this means that a single temperature factor will be defined for all atoms. If not then all values will be incremented up or down by a single value.

Defining groups for each residue with the NOTE BUSTER_COMBINE_RES card

Suppose you wish to define a grouped B factor for each side chain group in a protein. It would be possible to have a separate NOTE BUSTER_COMBINE cards for each residue but this would be really long winded. Instead use a:
NOTE BUSTER_COMBINE_RES <Parameter_code> <Set selection>
This takes a set of atoms divides them into individual residues and then defines a separate combine group for each. the set. <Parameter_code> code can be 'XYZ' or 'B' or 'OCC' (but not 'ALL')
<Set selection> is either the name of a BUSTER_SET or an atom selection in curly brackets (explanation).

Example - you want to use a separate COMBINE B group for the side chain atoms from each residue. You also want the same for the main chain atoms for each residue. This can be done by specifying:
NOTE BUSTER_COMBINE_RES B Side
NOTE BUSTER_COMBINE_RES B Back
Note that the BUSTER sets Back and Side are automatically defined. Also if a particular residue only has one atom in the side chain (eg CB of an ALA) then no COMBINE group would be defined - as a minimum of two atoms are required. It is also possible to use NOTE BUSTER_COMBINE_RES to define individual rigid bodies for each residue. In this case a minimum of 3 atoms is required - otherwise no group is defined.

Resetting previous parameter selection with the NOTE BUSTER_RESET_CONSTANT_COMBINE card

NOTE BUSTER_RESET_CONSTANT_COMBINE
It can sometimes be useful to disregard CONSTANT, COMBINE, NOTE BUSTER_CONSTANT and NOTE BUSTER_COMBINE cards that have been produced by automatic scripts. This card can be used to get gelly to ignore all such cards that precede it. Other definitions can be specified after this.

As an example let's continue developing the occupancy refinement example above.
NOTE BUSTER_RESET_CONSTANT_COMBINE
NOTE BUSTER_SET Ligand = { A|500 }
NOTE BUSTER_SET NotLigand = \ Ligand
NOTE BUSTER_CONSTANT OCC NotLigand
NOTE BUSTER_CONSTANT XYZ NotLigand
NOTE BUSTER_CONSTANT B NotLigand
NOTE BUSTER_COMBINE OCC Ligand
NOTE BUSTER_COMBINE B Ligand
The first command specifies that gelly should disregard all previous constant and combines found. It then defines the ligand to be residue 500 from chain A. The xyz coordinates, temperature factors and occupancies of all non-Ligand atoms are held fixed. A single occupancy and temperature factor is used for the ligand. The net result is that the ligand will be able to refine its atomic positions, a temperature factor and an occupancy within a rigid protein. This means that a single temperature factor will be defined for all atoms.
Page Author: Oliver S. Smart
Please send feedback to: buster-develop@globalphasing.com
Last modification: 10.07.08