Supporting Data mmcif_em.dic

Dictionary Revision History

Version Revision Date Revision Description
0.015 2013-1018 Changes (jdw):
+ Dictionary description updated.
0.014 2007-11-19 Changes: (jdw/cl)
+ update example for category em_array_formation
+ miscellaneous corrections
0.013 2005-10-14 Changes: (jdw)
+ Remove more special characters from enumerations.
+ Renamed iims -> em
0.012 2005-08-23 Changes: (jdw)
+ Remove non-ascii characters from description text.
0.011 2005-07-29 Changes: (jdw)
+ Corrections to v0.010
+ Implemented changes recommended by Bridget Carragher and Ron Milligan
0.010 2005-07-28 Changes: (jdw)
+ Implemented changes recommended by Wah Chiu, Matt Baker, and Cathy Lawson.
0.009 2005-07-13 Changes: (jdw)
+ Added Cathy Lawson's revised definitions and examples.
0.008 2005-06-09 Changes: (jdw)
+ revise category keys in em_image_selection group
0.007 2005-06-09 Changes: (jdw)
+ Reorganize em_sample_description_group
+ Reorganize em_data_collection_group
+ Reorganize em_image_selection_group
+ Detailed particle list categories temporarily removed from this version.
0.006 2005-06-01 Changes: (jdw)
+ Add category groups
+ Add changes proposed by EM Workshop participants.
0.005 2004-12-04 Changes:
+ Added em_electron_diffraction, em_electron_diffraction_phasing, and
em_electron_diffraction_pattern
+ Miscellaneous corrections.
0.004 2004-11-03 Changes:
+ Reflects revisions from EM Workshop Oct 2004.
0.003 2004-10-10 Changes: (jdw)
+ Adjust enumerations
0.002 2004-04-15 Changes: (jdw)
+ Added partitioning and dictionary revision history.
+ Fix syntax errors in category examples.
+ Added missing units.
0.001 2001-09-21
Initial version.
Data Type Code Primitive Type Code Regular Expression Description
any char .* A catch all for items that may take any form...
atcode char [][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* Character data type for atom names ...
code char [_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words ...
float numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? int item types are the subset of numbers that are the floating
numbers.
idname uchar [_A-Za-z0-9]+ idname item types take the form...
int numb -?[0-9]+ int item types are the subset of numbers that are the negative
or positive integers.
line char [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items ...
name uchar _[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+ name item types take the form...
symop char ([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])? symop item types take the form n_klm, where n refers to the
symmetry operation that is applied to the coordinates in the
ATOM_SITE category identified by _atom_site_label. It must
match a number given in _symmetry_equiv_pos_site_id.

k, l, and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used. These translations (x,y,z) are related to
(k,l,m) by
k = 5 + x
l = 5 + y
m = 5 + z
By adding 5 to the translations, the use of negative numbers
is avoided.
text char [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* text item types / multi-line text ...
uchar1 uchar [+]?[A-Za-z0-9]
data item for 1 character codes
uchar3 uchar [+]?[A-Za-z0-9][A-Za-z0-9][A-Za-z0-9]
data item for 3 character codes
ucode uchar [_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
uline uchar [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items (case insensitive)...
yyyy-mm-dd char [0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]
Standard format for CIF dates.
SubCategory Identifier Description
cartesian_coordinate The collection of x, y, and z components of a position specified
with reference to a Cartesian (orthogonal angstrom) coordinate
system.
cartesian_coordinate_esd The collection of estimated standard deviations of the x, y, and
z components of a position specified with reference to a
Cartesian (orthogonal angstrom) coordinate system.
cell_angle The collection of alpha, beta, and gamma angles of a unit cell.
cell_angle_esd The collection of estimated standard deviations of the alpha,
beta, and gamma angles of a unit cell.
cell_length The collection of a, b, and c axis lengths of a unit cell.
cell_length_esd The collection of estimated standard deviations of the a, b, and
c axis lengths of a unit cell.
fractional_coordinate The collection of x, y, and z components of a position specified
with reference to unit cell directions.
fractional_coordinate_esd The collection of estimated standard deviations of the x, y, and
z components of a position specified with reference to unit cell
directions.
matrix The collection of elements of a matrix.
miller_index The collection of h, k, and l components of the Miller index of
a reflection.
mm_atom_site_auth_label The collection of asym id, atom id, comp id and seq id
components of an author's alternative specification for
a macromolecular atom site.
mm_atom_site_label The collection of alt id, asym id, atom id, comp id and seq id
components of the label for a macromolecular atom site.
vector The collection of elements of a vector.
Units Identifier Description
8pi2_angstroms_squared 8pi2 * angstroms squared (meters * 10(-10))2
angstroms angstroms (meters * 10(-10))
angstroms_cubed angstroms cubed (meters * 10(-10))3
angstroms_squared angstroms squared (meters * 10(-10))2
arbitrary arbitrary system of units.
celsius degrees (of temperature) Celsius
centimetres centimetres (meters * 10( -2))
daltons daltons
degrees degrees (of arc)
degrees_per_minute degrees (of arc) per minute
electron_volts electron volts
electrons electrons
electrons_angstrom_squared electrons square angstrom
electrons_per_angstroms_cubed electrons per angstroms cubed (meters * 10(-10))3
electrons_per_nanometres_cubed electrons per nanometres cubed (meters * 10( -9))3
electrons_per_picometres_cubed electrons per picometres cubed (meters * 10(-12))3
electrons_squared electrons squared
femtometres femtometres (meters * 10(-15))
gigapascals gigapascals
hours hours
kelvins degrees (of temperature) Kelvin
kilopascals kilopascals
kilovolts kilovolts
kilowatts kilowatts
megadaltons megadaltons
mg_per_ml milligram per milliliter
microns microns
microns_squared microns squared
microseconds microseconds
milliamperes milliamperes
millimetres millimetres (meters * 10( -3))
millimolar millimolar
minutes minutes
nanometres nanometres (meters * 10( -9))
nanometres_cubed nanometres cubed (meters * 10( -9))3
nanometres_squared nanometres squared (meters * 10( -9))2
picometres picometres (meters * 10(-12))
picometres_cubed picometres cubed (meters * 10(-12))3
picometres_squared picometres squared (meters * 10(-12))2
reciprocal_angstroms reciprocal angstroms (meters * 10(-10)-1)
reciprocal_centimetres reciprocal centimetres (meters * 10( -2)-1)
reciprocal_millimetres reciprocal millimetres (meters * 10( -3)-1)
reciprocal_nanometres reciprocal nanometres (meters * 10( -9)-1)
reciprocal_picometres reciprocal picometres (meters * 10(-12)-1)
seconds seconds

Units Conversion List

From Units&Identifier To Units&Identifier Operator Conversion Factor
centimetres millimetres * 1.0E+01
centimetres nanometres * 1.0E+07
centimetres angstroms * 1.0E+08
centimetres picometres * 1.0E+10
centimetres femtometres * 1.0E+13
millimetres centimetres * 1.0E-01
millimetres nanometres * 1.0E+06
millimetres angstroms * 1.0E+07
millimetres picometres * 1.0E+09
millimetres femtometres * 1.0E+12
nanometres centimetres * 1.0E-07
nanometres millimetres * 1.0E-06
nanometres angstroms * 1.0E+01
nanometres picometres * 1.0E+03
nanometres femtometres * 1.0E+06
angstroms centimetres * 1.0E-08
angstroms millimetres * 1.0E-07
angstroms nanometres * 1.0E-01
angstroms picometres * 1.0E+02
angstroms femtometres * 1.0E+05
picometres centimetres * 1.0E-10
picometres millimetres * 1.0E-09
picometres nanometres * 1.0E-03
picometres angstroms * 1.0E-02
picometres femtometres * 1.0E+03
femtometres centimetres * 1.0E-13
femtometres millimetres * 1.0E-12
femtometres nanometres * 1.0E-06
femtometres angstroms * 1.0E-05
femtometres picometres * 1.0E-03
reciprocal_centimetres reciprocal_millimetres * 1.0E-01
reciprocal_centimetres reciprocal_nanometres * 1.0E-07
reciprocal_centimetres reciprocal_angstroms * 1.0E-08
reciprocal_centimetres reciprocal_picometres * 1.0E-10
reciprocal_millimetres reciprocal_centimetres * 1.0E+01
reciprocal_millimetres reciprocal_nanometres * 1.0E-06
reciprocal_millimetres reciprocal_angstroms * 1.0E-07
reciprocal_millimetres reciprocal_picometres * 1.0E-09
reciprocal_nanometres reciprocal_centimetres * 1.0E+07
reciprocal_nanometres reciprocal_millimetres * 1.0E+06
reciprocal_nanometres reciprocal_angstroms * 1.0E-01
reciprocal_nanometres reciprocal_picometres * 1.0E-03
reciprocal_angstroms reciprocal_centimetres * 1.0E+08
reciprocal_angstroms reciprocal_millimetres * 1.0E+07
reciprocal_angstroms reciprocal_nanometres * 1.0E+01
reciprocal_angstroms reciprocal_picometres * 1.0E-02
reciprocal_picometres reciprocal_centimetres * 1.0E+10
reciprocal_picometres reciprocal_millimetres * 1.0E+09
reciprocal_picometres reciprocal_nanometres * 1.0E+03
reciprocal_picometres reciprocal_angstroms * 1.0E+01
nanometres_squared angstroms_squared * 1.0E+02
nanometres_squared picometres_squared * 1.0E+06
angstroms_squared nanometres_squared * 1.0E-02
angstroms_squared picometres_squared * 1.0E+04
angstroms_squared 8pi2_angstroms_squared * 78.9568
picometres_squared nanometres_squared * 1.0E-06
picometres_squared angstroms_squared * 1.0E-04
nanometres_cubed angstroms_cubed * 1.0E+03
nanometres_cubed picometres_cubed * 1.0E+09
angstroms_cubed nanometres_cubed * 1.0E-03
angstroms_cubed picometres_cubed * 1.0E+06
picometres_cubed nanometres_cubed * 1.0E-09
picometres_cubed angstroms_cubed * 1.0E-06
kilopascals gigapascals * 1.0E-06
gigapascals kilopascals * 1.0E+06
hours minutes * 6.0E+01
hours seconds * 3.6E+03
hours microseconds * 3.6E+09
minutes hours / 6.0E+01
minutes seconds * 6.0E+01
minutes microseconds * 6.0E+07
seconds hours / 3.6E+03
seconds minutes / 6.0E+01
seconds microseconds * 1.0E+06
microseconds hours / 3.6E+09
microseconds minutes / 6.0E+07
microseconds seconds / 1.0E+06
celsius kelvins - 273.0
kelvins celsius + 273.0
electrons_per_nanometres_cubed electrons_per_angstroms_cubed * 1.0E-03
electrons_per_nanometres_cubed electrons_per_picometres_cubed * 1.0E-09
electrons_per_angstroms_cubed electrons_per_nanometres_cubed * 1.0E+03
electrons_per_angstroms_cubed electrons_per_picometres_cubed * 1.0E-06
electrons_per_picometres_cubed electrons_per_nanometres_cubed * 1.0E+09
electrons_per_picometres_cubed electrons_per_angstroms_cubed * 1.0E+06