selection selection {
}
adds a single cross-peak intensity or a
buildup curve between the two
specified selected sets of spins. The number of mixing times
read depends on the number of CLASs statements issued before the
ASSIgn statement.
Error estimates can be specified. The
format depends on the ERROr_input statement. For
examples, see Section 39.7.
AVERage real
specifies an exponent for calculating the
average distance to an UNREsolved group of protons (default: 6).
CALIbrate { calibrate-statement } END
calculates the calibration
factor between the observed and calculated intensities. Prior to the
calibration, this command computes the NOE intensities from the current
atomic model unless VALUe is specified.
calibrate-statement:==
AUTOmatic=ON,OFF
sets the calibration factor, if ON,
every step during the refinement. At present, this allows the calculation
of the gradient only approximately. Therefore, it should be turned OFF during
minimization.
GROUp=CLASs,GROUp,ALL
for CLASS, calculates the
calibration factor
separately for each classification; for ALL, one overall
calibration factor is used (default: CLASs).
QUALity=real
specifies that cross peaks for which the
relative error estimate exceeds the specified value are not used (default: 1).
REFErence=ALL,REFErence
for ALL, uses all peaks that
meet the criterion set with the EXCLude option for the
calculation of the calibration factor; for REFErence, uses only those
that were flagged as reference peaks during input (default: ALL).
VALUe class *real*
sets a value for the calibration factor.
Note: if the calibration factor is set by VALUe for
a class, it is not recalculated for other classes
in the same CALIbrate statement.
CLASsification class-name
partitions an intensity
table; it applies to all following ASSIgn entries
until another CLASS entry is issued.
In contrast to the NOE CLASs statement, the RELAxation CLASs
statement can be used to switch between classes during the input
of cross-peak intensities. Several class statements can be
issued without an intervening ASSIgn statement. This allows
the input of buildup curves (default: NIL).
CLGR (CLass_GRoup) *class* group
enters a CLASs into a GROUp of spectra (default: none).
CUTOff
{ cutoff-statement } END applies a cutoff to
relaxation matrix and/or gradient calculation. When a cutoff is in
effect, for each peak
on the data list a separate small relaxation matrix is set up,
including only spins
within a range of the spin pair specified by the cutoff.
The spectrum and the gradient are calculated with this
small relaxation matrix.
cutoff-statement:==
MODE=NONE,GRADient,ALL
applies no cutoff, cutoff only
for the
gradient calculation, or cutoff for both intensity and gradient
calculation
(default: NONE).
RELAtive_value=real
specifies a cutoff relative to the actual distance
between the two spins in Å (default: 0).
VALUe=real
specifies the actual value of the cutoff,
in Å (default: 6).
EEXPonent real
is an exponent of the WELL or
PARAbolic energy function (default: 2).
ERROr_input
{ error-input-statement } END
defines an error input format for the following ASSIgn statement.
It remains in effect until another ERROr_input command is
issued.
errorinput-statement:==
INPUt=UNIForm,RANGe,PLUSminus
specifies the
input format (0, 1, or 2
error estimates) for the following ASSIgn statements
(default: RANGe): for UNIForm, no error estimate is expected
by the program, for RANGe, one error estimate, and for PLUSminus,
two, where the first is an error estimate on the minus side, the second on the plus side.
MODE=ABSOlute,RELAtive
interprets the error estimate in the
ASSIgn statements as absolute or relative
(default: ABSOlute).
VALUe=real
enters the actual value for UNIForm option
(default: 0).
GROUp group-name
defines a group of several
CLASses that are recorded with the same physical conditions,
like solvent(HO, DO), field strength, and temperature
(default: NIL).
IEXPonent real
specifies an exponent of the calculated and
observed intensities in the energy function (default: 1).
IWEIght
{ iweight-statement } END applies
individual weights to each single term in the energy function.
At the moment, the only supported options are weights equal to the inverse
of
powers of the observed intensity (i.e.,
).
If the exponent matches the exponent of the energy
function, the weighting is equivalent to refining relative intensity
differences. The minimum weight applied is always 1.
iweight-statement:==
CUTOff=real
is the maximum weight applied (default: 10000).
EXPOnent=real
specifies an exponent of the
observed intensity in the weight function
(default: 2).
QUALity=real
stipulates that cross peaks for which the
relative error estimate exceeds the specified value are not used in
determining the maximum weight (default: 1).
MINIntensity *class* real
sets the minimum
detected intensity for each class.
The specified value is used as the “zero" for the intensities (default:
smallest number used by X-PLOR).
NREStraints integer
is the required parameter that specifies
the maximum expected number of intensities.
It has to be greater than or equal to the actual number. The parameter is
used to
assign space dynamically for the intensity list (default: 200).
OCCUpancy group selection real
sets
the occupancy for selected spins (for example, 0.9 for exchanging
amid protons) (default: 1.0).
OMEGa *group* real
specifies the spectrometer frequency, in Hz
(default: 500*10).
OMIT group selection
is an obsolete statement
that was used
in a prerelease version of the relaxation matrix code of X-PLOR. It will
be removed in a future version. The statement deletes spins from the
relaxation matrix. This is almost the reverse of the SELEct
command, but it leaves any existing base of unresolved groups
intact (default: none).
POTEntial WELL,PARAbolic
provides two alternatives: WELL uses a flat-bottom
potential with bounds at error estimates, PARAbolic a
(generalized) parabola with exponent EEXP and center at
the specified intensity (default: WELL).
PREDict_intensities
class
{ predict-intensities-statement } END
calculates a spectrum from coordinates with the parameters valid for the
specified class. Note that this destroys any existing experimental intensity database.
The spectrum can be calculated for parts of a molecular structure.
PREDict_intensities-statement:==
CUTOFf real
specifies a distance cutoff for cross-peak
calculation (default: 10).
CUTON real
specifies a distance cuton for cross-peak
calculation (default: 0).
DIAGonal ON,OFF
prints diagonal peaks (default: OFF).
FORMat NORMal,LIST
is an output format; LIST produces
an intensity INPUT file (default: NORMal).
FROM selection
selects the first part of a molecular structure
(default: all NMR-active atoms).
THREshold real
specifies the minimum intensity that is printed (default: 0).
TO selection
selects the second part of a molecular structure
(default: all NMR-active atoms).
PRINt_deviations
{ print-deviation-statement } END
prints the deviations from observed intensities and calculates
an value. It uses the form of the energy function
(WELL or PARAbolic and the value of IEXP) specified
before issuing the statement.
print-deviation-statement:==
FORMat NORMal,LIST
is an output format; LIST produces
a listing in the format of an intensity input file.
SELEct selection
calculates the value with only a
subset of the atoms. This allows the calculation of
local values.
THREshold real
specifies the minimum deviation that is printed,
in the arbitrary units of the input intensities.
For a complete list of deviations (including 0), THREshold
should be set to a negative number (default: 0).
REFErence
flags intensities read by the
following ASSIgn
statements as reference peaks for the calculation of the calibration
factor (see CALIbrate statement),
and remains in effect until another CLASs statement is issued.
This flag allows one to use a subset of peaks for the calibration,
e.g., peaks that do not depend very much on the conformation
of the molecule.
The reference peaks are written into a separate file,
and the reference flag is set before reading that file.
RESEt
erases the current relaxation database.
SELEct group selection
selects the “NMR-active"
atoms (default: (HYDRogen) ).
At present, only protons can be used in the refinement. The
NMR parameters for protons are applied to all selected atoms.
This command initializes the array that stores information about
unresolved groups (see below).
If the command is not issued at the beginning of the relaxation matrix setup,
all hydrogens are used by default. Since a hydrogen is defined by
its mass in X-PLOR, care should be taken in this case to modify the
masses of hydrogens for simulated
annealing only after the relaxation matrix parameters
have been set up.
SORT_intensities
sorts the
intensity list so that peaks with different mixing times
belonging to the same spin pair are consecutive on the list.
If a cutoff is used, a new relaxation matrix generally has to be set up and
diagonalized for each peak on the data list. However,
if the only difference between two entries on the data list is the mixing time,
the relaxation matrix does not have
to be recalculated and diagonalized. Sorting can thus save a considerable
amount of CPU time.
TAUCorrelation
group { TAUC-statement } END
specifies the correlation time and the order parameter, depending
on the chosen model.
TAUCorrelation-statement:==
MODEl RIGIdLIPAri
provides two alternatives: RIGId
expects no order parameter;
LIPAri expects one overall correlation time and one order parameter.
This applies to both the ISOTropic and the VECTor case.
ISOTropic
specifies an
isotropic correlation time
and an order parameter (default: 10 ns, 1).
RESEt
initializes a table.
VECTor selection selection
specifies a
correlation time
(in seconds) and an order
parameter for a specified vector.
TAUMix *class* real
specifies the mixing time
, in seconds (default: 0.1 sec).
TOLErance real
if not equal to zero,
approximates the exact calculation of the
energy function and its first
derivatives with respect to the atomic coordinates
by freezing
until atoms
have moved by less than TOLErance Å from the point at which
was
last computed. This is particularly useful for
molecular dynamics calculations. It should be set to 0
during minimization to avoid inconsistencies
in the force field (default: 0).
UPDate
computes the NOE intensities from the current atomic model.
UNREsolved
group { unresolved-statement } END
replaces protons with unresolved chemical shifts by a single
spin. The distance to an unresolved group is calculated
as
, where the exponent is set with the
AVERage command. A diagonal leakage rate is added
to the relaxation matrix for each unresolved group.
The main use of this command is for methyl groups.
unresolved-statement:==
1-2
treats each methylene group as an unresolved group of
protons. A methylene group is recognized by
X-PLOR as two hydrogens bound to a heavy
atom.
METHyl
treats each methyl group as an unresolved group of
protons. A methyl group is recognized by
X-PLOR as three hydrogens bound to a
heavy atom.
NONE
deletes all previously defined unresolved groups.
SELECT selection
treats the selected atoms as
an unresolved group of protons.
WEIGht *class* real
specifies the
energy constant (overall weight)
(default: 1).
ZLEAkage_rate *group*
specifies the overall diagonal
leakage rate , in sec
(default: 0).