Data Item _array_intensities.linearity

General

Item name
_array_intensities.linearity
Category name
array_intensities
Attribute name
linearity
Required in PDB entries
yes
Used in currrent PDB entries
No

Item Description

The intensity linearity scaling method used to convert from the raw intensity to the stored element value: 'linear' is linear. 'offset' means that the value defined by _array_intensities.offset should be added to each element value. 'scaling' means that the value defined by _array_intensities.scaling should be multiplied with each element value. 'scaling_offset' is the combination of the two previous cases, with the scale factor applied before the offset value. 'sqrt_scaled' means that the square root of raw intensities multiplied by _array_intensities.scaling is calculated and stored, perhaps rounded to the nearest integer. Thus, linearization involves dividing the stored values by _array_intensities.scaling and squaring the result. 'logarithmic_scaled' means that the logarithm base 10 of raw intensities multiplied by _array_intensities.scaling is calculated and stored, perhaps rounded to the nearest integer. Thus, linearization involves dividing the stored values by _array_intensities.scaling and calculating 10 to the power of this number. 'raw' means that the data are a set of raw values straight from the detector.

Data Type

Data type code
code
Data type detail
code item types/single words ...
Primitive data type code
char
Regular expression
[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*

Controlled Vocabulary

Allowed Value Details
linear
logarithmic_scaled The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
offset The value defined by _array_intensities.offset should
be added to each element value.
raw The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
scaling The value defined by _array_intensities.scaling should be
multiplied with each element value.
scaling_offset The combination of the scaling and offset
with the scale factor applied before the offset value.
sqrt_scaled The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.

Controlled Vocabulary at Deposition

Allowed Value Details
linear
logarithmic_scaled The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
offset The value defined by _array_intensities.offset should
be added to each element value.
raw The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
scaling The value defined by _array_intensities.scaling should be
multiplied with each element value.
scaling_offset The combination of the scaling and offset
with the scale factor applied before the offset value.
sqrt_scaled The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.