The project is funded by the European Commission as the IIMS,
contract-no. QLRI-CT-2000-31237 under the RTD programme
"Quality of Life and Management of Living Resources"
This document tabulates the correspondences between data items in the structured records of the PDB file format and data items defined in the mmCIF dictionary. The structured records in the following list are linked to tables which provide the data item correspondences. The mmCIF data items are in term linked to their definitions in the HTML mmCIF dictionary.
| Remark Field Name | mmCIF Data Item | |
|---|---|---|
| REMARK 3, REFINEMENT | ||
| SOFTWARE PACKAGES : | _em_2d_projection_selection.software_name | |
| RECONSTRUCTION SCHEMA : | _em_3d_reconstruction.method | |
| EM MAP-MODEL FITTING AND REFINEMENT | ||
| PDB ENTRY : | _3d_fitting_list.pdb_entry_id | |
| REFINEMENT SPACE : | _3d_fitting.ref_space | |
| REFINEMENT PROTOCOL : | _3d_fitting.ref_protocol | |
| REFINEMENT TARGET : | _3d_fitting.target_criteria | |
| OVERALL ANISOTROPIC B VALUE : | _3d_fitting.overall_b_value | |
| FITTING PROCEDURE : | _3d_fitting.method | |
| EM IMAGE RECONSTRUCTION STATISTICS | ||
| NOMINAL PIXEL SIZE (ANGSTROMS) : | _em_3d_reconstruction.nominal_pixel_size | |
| ACTUAL PIXEL SIZE (ANGSTROMS) : | _em_3d_reconstruction.actual_pixel_size | |
| EFFECTIVE RESOLUTION (ANGSTROMS) : | _em_3d_reconstruction.resolution | |
| NUMBER OF PARTICLES : | _em_2d_projection_selection.num_particles | |
| CTF CORRECTION METHOD : | _em_3d_reconstruction.ctf_correction_method | |
| EM RECONSTRUCTION MAGNIFICATION CALIBRATION : | _em_3d_reconstruction.magnification_calibration | |
| OTHER DETAILS : | _em_3d_reconstruction.details |
| Remark Field Name | mmCIF Data Item | |
|---|---|---|
| REMARK 245, EXPERIMENTAL DETAILS | ||
| EXPERIMENT TYPE: CRYO-ELECTRON MICROSCOPY | _exptl.method | |
| ELECTRON MICROSCOPE SAMPLE | ||
| SAMPLE AGGREGATION STATE : | _assembly.aggregation_state | |
| NAME OF SAMPLE : | _assembly.name | |
| SAMPLE CONCENTRATION : | _em_sample_preparation.sample_concentration | |
| SAMPLE SUPPORT DETAILS : | _em_sample_support.details | |
| SAMPLE VITRIFICATION DETAILS : | _em_sample_vitrification.details | |
| SAMPLE BUFFER : | _em_sample_buffer.name | |
| PH : | _em_sample_preparation.ph | |
| SAMPLE DETAILS : | _assembly.details | |
| DATA ACQUISITION | ||
| DATE OF EXPERIMENT : | _em_imaging.date | |
| NUMBER OF MICROGRAPHS-IMAGES USED : | _em_image_scans.number_digital_images | |
| TEMPERATURE (KELVIN) : | _em_imaging.temperature | |
| MICROSCOPE MODEL : | _em_imaging.microscope_model | |
| DETECTOR TYPE : | _em_detector.type | |
| MINIMUM DEFOCUS (NM) : | _em_imaging.nominal_defocus_min | |
| MAXIMUM DEFOCUS (NM) : | _em_imaging.nominal_defocus_max | |
| MINIMUM TILT ANGLE (DEGREES) : | _em_imaging.tilt_angle_min | |
| MAXIMUM TILT ANGLE (DEGREES) : | _em_imaging.tilt_angle_max | |
| NOMINAL CS : | _em_imaging.nominal_cs | |
| IMAGING MODE : | _em_imaging.mode | |
| ELECTRON DOSE (ELECTRONS NM**-2) : | _em_imaging.electron_dose | |
| ILLUMINATION MODE : | _em_imaging.illumination_mode | |
| NOMINAL MAGNIFICATION : | _em_imaging.nominal_magnification | |
| CALIBRATED MAGNIFICATION : | _em_imaging.calibrated_magnification | |
| SOURCE : | _em_imaging.electron_source | |
| ACCELERATION VOLTAGE (KV) : | _em_imaging.accelerating_voltage | |
| IMAGING DETAILS : | _em_imaging.details |
| Remark Field Name | mmCIF Data Item | |
|---|---|---|
| REMARK 300, BIOMOLECULE | ||
| ASSEMBLY COMPONENTS | ||
| COM_ID : | _entity_assembly.id | |
| NAME : | _entity_assembly.name | |
| IPR_ID : | _entity_assembly.ipr_id | |
| GO_ID : | _entity_assembly.go_id | |
| OTHER DETAILS: | _entity_assembly.details | |
| VIRUS PARTICULARS. | ||
| COM_ID : | _virus_entity.entity_assembly_id | |
| VIRUS_HOST_CATEGORY : | _virus_entity.virus_host_category | |
| VIRUS_HOST_SPECIES : | _virus_entity.virus_host_species | |
| VIRUS_HOST_GROWTH_CELL : | _virus_entity.virus_host_growth_cell | |
| VIRUS_TYPE : | _virus_entity.virus_type | |
| VIRUS_ISOLATE : | _virus_entity.virus_isolate | |
| ICTVDB_ID : | _virus_entity.ictvdb_id |
The project is funded by the European Commission as the IIMS,
contract-no. QLRI-CT-2000-31237 under the RTD programme
"Quality of Life and Management of Living Resources"