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Appendix D: Utility restraint terms in gelly
Copyright © 2006-2016 Global Phasing Ltd.
All rights reserved.
Contents
As well as all the restraints that are defined by TNT-type restraint dictionaries for input
molecules gelly allows the definition of a number of "utility" restraints
that can be used a user to allow finer control of refinement. It is intended to
add more of these terms in the future. If you would like a restraint on any particular
feature then let us know.
It can be useful to be able to restrain the distance between two given atoms.
For instance such restraints can be used to ensure secondary structure is maintained
in the initial cycles of refinement. The NOTE BUSTER_DISTANCE
allows the specification of a harmonic restraint on the distance
between any two atoms to a given target with a given sigma.
The restraint can be half-harmonic, that is only apply if the distance
strays above (or alternatively below) the target. It can be specified:
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NOTE BUSTER_DISTANCE +3.0 0.02 A|10:O A|14:N
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This card means that a large penalty will be applied if the distance between
mainchain O of residues A|10 and N of A|14 goes ABOVE 3.0 angstroms.
The sigma for the restraint is 0.02 angstroms (as strong as a typical bond).
Such restraints can be used to maintain expected helical secondary structure.
To restrain a distance to be equal to a target value use an = in place of + for example:
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NOTE BUSTER_DISTANCE =3.0 0.02 A|10:O A|14:N
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To have apply a restraint only if two atoms come below a certain distance then use - instead.
Note that using a distance restraint between two atoms does not effect any short contacts between them - this
can be controlled using the TNT EXCLUDE card.
A practical example demonstrating the use of NOTE BUSTER_DISTANCE cards
can be found in the
forcing a zinc ion site to be tetrahedral
example found at the
Global Phasing BUSTER Wiki.
A new feature introduced in the November 2011 release of BUSTER is to be able to specify a utility distance
restraint to an atom across a cell/symmetry operation. The main use for this kind of restraint is to
prevent an atom drifting from a special position or axis. To specify that a restraint is across a symmetry
operator add SYMM to the end of the NOTE BUSTER_DISTANCE. The SYMM means
that the distance restraint will be to a symmetry copy of the 2nd atom. All symmetry operations
including lattice translations are checked (other than the identity) and which ever gives the smallest
distance is chosen (if two or more operations give the same distance the first one found is chosen). As an example
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NOTE BUSTER_DISTANCE +0.001 0.02 A|457:O A|457:O SYMM
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This would be used for a water molecule on a special position. The restraint is
on the distance between the water molecule and its closest symmetry equivalent. If this distance
is above 1/1000 th Angstrom then a harmonic restraint is applied reducing the distance with
a sigma of 0.02 Angstroms. The effect of this will be to strongly pull the atom and its symmetry equivalent
together. Note that in the case of a symmetry axis the atom will still be able to move along the axis.
For further details on the handling of special position atoms and ions see
Appendix F: Handling special position atoms and ions.
A practical example demonstrating the use of NOTE BUSTER_DISTANCE cards
can be found in the
Handling Special Position atoms and ions
example found at the
Global Phasing BUSTER Wiki.
Details as to the operator setup by SYMM can be found in the LIST.html output file in a section
like:
Setup symmetry for utility distance restraints (NOTE BUSTER_DISTANCE)
A 457 O to symmetry copy of A 457 O SYMM specified so found operator 3555 gave minimum distance= 1.129
D 581 O to symmetry copy of D 581 O SYMM specified so found operator 3545 gave minimum distance= 0.332
E 1244O to symmetry copy of E 1244O SYMM specified so found operator 8555 gave minimum distance= 0.129
Although it is seldom necessary it is also possible to use a specified symmetry operator for a restraint. The operator
wanted is specified in "PDB convention" (where 1555 is the identity operator) the end of the line.
For instance:
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NOTE BUSTER_DISTANCE +0.001 0.02 A|457:O1 A|457:O2 3665
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This would apply a restraint reducing the distance between atom O1 of residue 457 and atom O2 of the
same residue but through the specific 3rd symmetry operator (see output PDB file) and the translation vector
110 . Fortunately is it seldom necessary to use a specific operator - try SYMM in the first
instance.
This restraint is on the angle between any three atoms. This could be a bond angle but need not be. For example:
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NOTE BUSTER_UTILANGLE 109.5 4.0 B|109:SG B|154:ZN B|114:SG
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This places a harmonic restraint on the angle between the three atoms from the B chain
SG from residue 109, ZN residue 154 and SG from residue 114. The target value of the restraint is 109.5 degrees
and the sigma is 4 degrees.
Note that using angle restraint does not directly effect any short contacts - this
can be controlled using the TNT EXCLUDE card.
LIMITATION: currently cell/symmetry operations are ignored in UTILANGLE calculations
A practical example demonstrating the use of NOTE BUSTER_UTILANGLE cards
can be found in the
forcing a zinc ion site to be tetrahedral
example found at the
Global Phasing BUSTER Wiki.
LIMITATION: currently cell/symmetry operations are ignored in UTILTOR calculations
When refining occupancies it can be useful to ensure that the occupancies of alternative conformations
are restrained such that their sum is equal to a given value (normally 1.0). The NOTE BUSTER_OCCSUM
card imposes a restraint:
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V_occsum = K [ (Sum_i occ_i) - 1.0]^2
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where
Example:
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NOTE BUSTER_OCCSUM 1.0 0.005 H|1:CB.A H|1:CB.B
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This specifies that atoms CB.A and CB.B from residue 1 in chain H have a
restraint on the sum of their occupancies to equal 1.0. The sigma for the
restraint is 0.005
Page Author: Oliver S. Smart
Please send feedback to: buster-develop@globalphasing.com
Last modification: 29.06.2020
