Supporting Data mmcif_em.dic
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Dictionary Revision History
| Version | Revision Date | Revision Description | |
|---|---|---|---|
| 0.015 | 2013-1018 | Changes (jdw): + Dictionary description updated. |
mmcif_em.dic |
| 0.014 | 2007-11-19 | Changes: (jdw/cl) + update example for category em_array_formation + miscellaneous corrections |
mmcif_em.dic |
| 0.013 | 2005-10-14 | Changes: (jdw) + Remove more special characters from enumerations. + Renamed iims -> em |
mmcif_em.dic |
| 0.012 | 2005-08-23 | Changes: (jdw) + Remove non-ascii characters from description text. |
mmcif_em.dic |
| 0.011 | 2005-07-29 | Changes: (jdw) + Corrections to v0.010 + Implemented changes recommended by Bridget Carragher and Ron Milligan |
mmcif_em.dic |
| 0.010 | 2005-07-28 | Changes: (jdw) + Implemented changes recommended by Wah Chiu, Matt Baker, and Cathy Lawson. |
mmcif_em.dic |
| 0.009 | 2005-07-13 | Changes: (jdw) + Added Cathy Lawson's revised definitions and examples. |
mmcif_em.dic |
| 0.008 | 2005-06-09 | Changes: (jdw) + revise category keys in em_image_selection group |
mmcif_em.dic |
| 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. |
mmcif_em.dic |
| 0.006 | 2005-06-01 | Changes: (jdw) + Add category groups + Add changes proposed by EM Workshop participants. |
mmcif_em.dic |
| 0.005 | 2004-12-04 | Changes: + Added em_electron_diffraction, em_electron_diffraction_phasing, and em_electron_diffraction_pattern + Miscellaneous corrections. |
mmcif_em.dic |
| 0.004 | 2004-11-03 | Changes: + Reflects revisions from EM Workshop Oct 2004. |
mmcif_em.dic |
| 0.003 | 2004-10-10 | Changes: (jdw) + Adjust enumerations |
mmcif_em.dic |
| 0.002 | 2004-04-15 | Changes: (jdw) + Added partitioning and dictionary revision history. + Fix syntax errors in category examples. + Added missing units. |
mmcif_em.dic |
| 0.001 | 2001-09-21 | Initial version. |
mmcif_em.dic |
| 0.015 | 2013-1018 | Changes (jdw): + Dictionary description updated. |
mmcif_em.dic |
| 0.014 | 2007-11-19 | Changes: (jdw/cl) + update example for category em_array_formation + miscellaneous corrections |
mmcif_em.dic |
| 0.013 | 2005-10-14 | Changes: (jdw) + Remove more special characters from enumerations. + Renamed iims -> em |
mmcif_em.dic |
| 0.012 | 2005-08-23 | Changes: (jdw) + Remove non-ascii characters from description text. |
mmcif_em.dic |
| 0.011 | 2005-07-29 | Changes: (jdw) + Corrections to v0.010 + Implemented changes recommended by Bridget Carragher and Ron Milligan |
mmcif_em.dic |
| 0.010 | 2005-07-28 | Changes: (jdw) + Implemented changes recommended by Wah Chiu, Matt Baker, and Cathy Lawson. |
mmcif_em.dic |
| 0.009 | 2005-07-13 | Changes: (jdw) + Added Cathy Lawson's revised definitions and examples. |
mmcif_em.dic |
| 0.008 | 2005-06-09 | Changes: (jdw) + revise category keys in em_image_selection group |
mmcif_em.dic |
| 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. |
mmcif_em.dic |
| 0.006 | 2005-06-01 | Changes: (jdw) + Add category groups + Add changes proposed by EM Workshop participants. |
mmcif_em.dic |
| 0.005 | 2004-12-04 | Changes: + Added em_electron_diffraction, em_electron_diffraction_phasing, and em_electron_diffraction_pattern + Miscellaneous corrections. |
mmcif_em.dic |
| 0.004 | 2004-11-03 | Changes: + Reflects revisions from EM Workshop Oct 2004. |
mmcif_em.dic |
| 0.003 | 2004-10-10 | Changes: (jdw) + Adjust enumerations |
mmcif_em.dic |
| 0.002 | 2004-04-15 | Changes: (jdw) + Added partitioning and dictionary revision history. + Fix syntax errors in category examples. + Added missing units. |
mmcif_em.dic |
| 0.001 | 2001-09-21 | Initial version. |
mmcif_em.dic |
Data Type List
| 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 List
| 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 List
| 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 |