########################################################################### # # File: mmcif_biosync.dic # Date: Mon Aug 16 07:18:26 EDT 2021 # # Created from files in CVS module dict-mmcif_biosync.dic unless noted: # mmcif_biosync-header.dic # mmcif_biosync-data.dic # mmcif_biosync-def-1.dic # mmcif_biosync-def-ilg.dic # ########################################################################### ############################################################################## # # File: mmcif_biosync-header.dic # # BIOSYNC Dictionary Extension to the # Macromolecular CIF Dictionary # # This extension dictionary contains definitions describing the details of # synchrotron beamlines and beamline facilities. # # # Header Section # ############################################################################## data_mmcif_biosync.dic _datablock.id mmcif_biosync.dic _datablock.description ; This data block holds the BIOSYNC extension to the mmCIF data dictionary. ; _dictionary.title mmcif_biosync.dic _dictionary.version 0.7 _dictionary.datablock_id mmcif_biosync.dic ######################## ## DICTIONARY_HISTORY ## ######################## loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 0.1 2000-02-17 'Initial version' 0.2 2000-07-31 'Update, add versioning' 0.3 2000-08-01 'Revised application of beamline_id' 0.4 2001-01-24 'mmCIF aliases added' 0.5 2005-10-20 ; Changes (jdw): +Added items: _bsync_diffrn_measurement.special_capabilities _bsync_diffrn_measurement.other_instrumentation ; 0.6 2005-10-27 ; Changes (jdw): +Moved _bsync_diffrn_measurement.monochromator _bsync_diffrn_measurement.monochromator_crystal _bsync_diffrn_measurement.mirrors _bsync_diffrn_measurement.mirror_cutoff to category bsync_diffrn_radiation. ; 0.7 2008-05-29 ; Changes (jdw): + corrections to examples, set mandatory codes for key items. ; ### EOF mmcif_biosync-header.dic ############################################################################## # # File: mmcif_biosync-data.dic # # BIOSYNC Dictionary Extension to the # Macromolecular CIF Dictionary # # This extension dictionary contains definitions describing the details of # synchrotron beamlines and beamline facilities. # # # Data Section # ############################################################################## #################### ## ITEM_TYPE_LIST ## #################### # # # The regular expressions defined here are not compliant # with the POSIX 1003.2 standard as they include the # '\n' and '\t' special characters. These regular expressions # have been tested using the version 0.12 of Richard Stallman's # GNU regular expression libary in POSIX mode. # loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.detail code char '[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words ... ; line char '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items ... ; uline uchar '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items (case insensitive)... ; text char '[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; text item types / multi-line text ... ; int numb '-?[0-9]+' ; int item types are the subset of numbers that are the negative or positive integers. ; 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. ; 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. ; any char '.*' ; A catch all for items that may take any form... ; ##################### ## ITEM_UNITS_LIST ## ##################### loop_ _item_units_list.code _item_units_list.detail 'meters' . 'centimetres' 'centimetres (meters * 10^( -2))' 'millimetres' 'millimetres (meters * 10^( -3))' 'nanometres' 'nanometres (meters * 10^( -9))' 'angstroms' 'angstroms (meters * 10^(-10))' 'celsius' 'degrees (of temperature) Celsius' 'kelvins' 'degrees (of temperature) Kelvin' 'hours' 'hours' 'minutes' 'minutes' 'seconds' 'seconds' 'microseconds' 'microseconds' 'kilowatts' 'kilowatts' 'milliamperes' 'milliamperes' 'kilovolts' 'kilovolts' 'KeV' 'kiloelectron volts (electron volts * 10^(3)' ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description 'inclusive_group' . ; All categories ; 'bsync_group' . ; Categories which pertain to the BIOSYNC project ; ### EOF mmcif_biosync-data.dic #################### ## BSYNC_FACILITY ## #################### save_bsync_facility _category.description ; You must press the "Save General Synchrotron Information" button to save changes. Then, Use the "UPDATE PROFILE" button at the top of this page to have the changes appear on the BioSync web site. ; # Data items in the BSYNC_FACILITY category describe data collection sites. _category.id bsync_facility _category.mandatory_code no _category_key.name '_bsync_facility.id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_facility.id 'aps' _bsync_facility.name 'Advanced Photon Source' _bsync_facility.operation 'Argonne National Lab' _bsync_facility.details ; 3rd generation light source ... ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_facility.id _item_description.description ; The synchrotron name, acronym. ; loop_ _item.name _item.category_id _item.mandatory_code '_bsync_facility.id' bsync_facility yes '_bsync_beamline.facility_id' bsync_beamline yes '_bsync_facility_website.facility_id' bsync_facility_website yes _item_type.code code loop_ _item_examples.case 'aps' 'ssrl' loop_ _item_linked.parent_name _item_linked.child_name '_bsync_facility.id' '_bsync_facility_website.facility_id' '_bsync_facility.id' '_bsync_beamline.facility_id' save_ save__bsync_facility.name _item_description.description ; The full name of the synchrotron facility ; _item.name '_bsync_facility.name' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; Advanced Photon Source. ; save_ save__bsync_facility.location _item_description.description ; The location of the synchrotron facility. City, State ; _item.name '_bsync_facility.location' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; Argonne,IL ; save_ save__bsync_facility.street1 _item_description.description ; The street address of the synchrotron facility. ; _item.name '_bsync_facility.street1' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; 1 Cyclotron Road ; save_ save__bsync_facility.street2 _item_description.description ; The street address of the synchrotron facility. ; _item.name '_bsync_facility.street2' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; 1 Cyclotron Road ; save_ save__bsync_facility.zip _item_description.description ; The zip code address of the synchrotron facility. ; _item.name '_bsync_facility.zip' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; 1 Cyclotron Road ; save_ save__bsync_facility.location_details _item_description.description ; A more detailed description of the location of the synchrotron facility. ; _item.name '_bsync_facility.location_details' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; Argonne,IL ; save_ save__bsync_facility.operation _item_description.description ; The lab or university which operates the synchrotron. ; _item.name '_bsync_facility.operation' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; Brookhaven National Lab ; save_ save__bsync_facility.organization _item_description.description ; A paragraph describing the organization of the synchrotron. ; _item.name '_bsync_facility.organization' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; Participating Research Teams. ; save_ save__bsync_facility.website_url _item_description.description ; Site location (URL) ; _item.name '_bsync_facility.website_url' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text save_ save__bsync_facility.details _item_description.description ; A description of special aspects of the facility. ; _item.name '_bsync_facility.details' _item.category_id bsync_facility _item.mandatory_code no _item_type.code text _item_examples.case ; 3rd generation light source ; save_ #################################### ## BSYNC_FACILITY_CRYSTALLOGRAPHY ## #################################### save_bsync_facility_crystallography _category.description ; Data items in the BSYNC_FACILITY_CRYSTALLOGRAPHY category record details about any special crystallography facility, organization, or website. ; _category.id bsync_facility_crystallography _category.mandatory_code no loop_ _category_key.name '_bsync_facility_crystallography.facility_id' '_bsync_facility_crystallography.name' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - SSRL ; ; _bsync_facility_crystallography.facility_id ssrl _bsync_facility_crystallography.name ; Structural Molecular Biology ; _bsync_facility_crystallography.url 'http://smb.slac.stanford.edu/' ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__bsync_facility_crystallography.facility_id _item_description.description ; This data item is a pointer to _bsync_facility.id in the BSYNC_FACILITY category. ; _item.name '_bsync_facility_crystallography.facility_id' _item.mandatory_code yes _item_type.code code _item_examples.case ; APS ; save_ save__bsync_facility_crystallography.name _item_description.description ; Name of specialized organization or facility within the synchrotron organization that operates beamlines for crystallography ; _item.name '_bsync_facility_crystallography.name' _item.category_id bsync_facility_crystallography _item.mandatory_code yes _item_type.code text _item_examples.case ; SBC-CAT ; save_ save__bsync_facility_crystallography.category _item_description.description ; The category for the structural biology organization - structural genomics, crystallography group ; _item.name '_bsync_facility_crystallography.category' _item.category_id bsync_facility_crystallography _item.mandatory_code no _item_type.code text loop_ _item_enumeration.value 'Structural Genomics' 'Crystallography' 'Other' save_ save__bsync_facility_crystallography.url _item_description.description ; Website for the organization ; _item.name '_bsync_facility_crystallography.url' _item.category_id bsync_facility_crystallography _item.mandatory_code no _item_type.code text save_ save__bsync_facility_crystallography.description _item_description.description ; A brief description of the specialized organization or facility within the synchrotron organization that operates beamlines for crystallography ; _item.name '_bsync_facility_crystallography.description' _item.category_id bsync_facility_crystallography _item.mandatory_code no _item_type.code text save_ save__bsync_facility_crystallography.details _item_description.description ; More details about the specialized organization or facility within the synchrotron organization that operates beamlines for crystallography ; _item.name '_bsync_facility_crystallography.details' _item.category_id bsync_facility_crystallography _item.mandatory_code no _item_type.code text save_ save__bsync_facility_crystallography.logo _item_description.description ; Logo for the crystallography facility or website. ; _item.name '_bsync_facility_crystallography.logo' _item.category_id bsync_facility_crystallography _item.mandatory_code no _item_type.code text save_ ######################### ## BSYNC_FACILITY_NEWS ## ######################### save_bsync_facility_news _category.description ; Data items in the BSYNC_FACILITY_NEWS category record details meetings, workshops, applications deadlines, news and announcements. ; _category.id bsync_facility_news _category.mandatory_code no loop_ _category_key.name '_bsync_facility_news.facility_id' ## '_bsync_facility_news.name' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - SSRL ; ; _bsync_facility_news.facility_id ssrl _bsync_facility_news.url 'http://www-ssrl.slac.stanford.edu/welcome.html' _bsync_facility_news.details 'summer school for crystallographers' ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__bsync_facility_news.facility_id _item_description.description ; This data item is a pointer to _bsync_facility.id in the BSYNC_FACILITY category. ; _item.name '_bsync_facility_news.facility_id' _item.mandatory_code yes _item_type.code code save_ save__bsync_facility_news.date _item_description.description ; A date for the news item. The date format is yyyy-mm-dd. ; _item.name '_bsync_facility_news.date' _item.category_id bsync_facility_news _item.mandatory_code yes _item_type.code yyyy-mm-dd _item_examples.case '1990-07-12' save_ save__bsync_facility_news.details _item_description.description ; News or announcement description. ; _item.name '_bsync_facility_news.details' _item.category_id bsync_facility_news _item.mandatory_code no _item_type.code text save_ save__bsync_facility_news.title _item_description.description ; Title of news or announcement. ; _item.name '_bsync_facility_news.title' _item.category_id bsync_facility_news _item.mandatory_code no _item_type.code text save_ save__bsync_facility_news.url _item_description.description ; Site location (URL) for more information ; _item.name '_bsync_facility_news.url' _item.category_id bsync_facility_news _item.mandatory_code no _item_type.code text save_ #################### ## BSYNC_BEAMLINE ## #################### save_bsync_beamline _category.description ; You must press the "Save General Beamline Information" button to save changes. Then, Use the "UPDATE PROFILE" button at the top of this page to have the changes appear on the BioSync web site. ; # Data items in the BSYNC_BEAMLINE category describe data collection beamlines. _category.id bsync_beamline _category.mandatory_code no loop_ _category_key.name '_bsync_beamline.id' '_bsync_beamline.facility_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_beamline.id '19_ID' _bsync_beamline.facility_id 'aps' _bsync_beamline.owner 'SBC-CAT' _bsync_beamline.experiments MAD ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_beamline.facility_id _item_description.description ; This data item is a pointer to _bsync_facility.id in the BSYNC_FACILITY category. ; _item.name '_bsync_beamline.facility_id' _item.mandatory_code yes _item_type.code code save_ save__bsync_beamline.id _item_description.description ; A unique identifier for the beamline within a facility. ; loop_ _item.name _item.category_id _item.mandatory_code '_bsync_beamline.id' bsync_beamline yes '_bsync_diffrn_detector.beamline_id' bsync_diffrn_detector yes '_bsync_diffrn_radiation.beamline_id' bsync_diffrn_radiation yes '_bsync_diffrn_measurement.beamline_id' bsync_diffrn_measurement yes '_bsync_diffrn_source.beamline_id' bsync_diffrn_source yes '_bsync_software.beamline_id' bsync_software yes _item_type.code code loop_ _item_examples.case 1 2 3 loop_ _item_linked.parent_name _item_linked.child_name '_bsync_beamline.id' '_bsync_diffrn_detector.beamline_id' '_bsync_beamline.id' '_bsync_diffrn_radiation.beamline_id' '_bsync_beamline.id' '_bsync_diffrn_measurement.beamline_id' '_bsync_beamline.id' '_bsync_diffrn_source.beamline_id' '_bsync_beamline.id' '_bsync_software.beamline_id' loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_beamline.name _item_description.description ; The name of the beamline. ; _item.name '_bsync_beamline.name' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'XB11' '18-ID' save_ save__bsync_beamline.source_type _item_description.description ; This data item is a pointer to _bsync_diffrn_source.type in the BSYNC_DIFFRN_SOURCE category. ; _item.name '_bsync_beamline.source_type' _item.mandatory_code yes _item_type.code text save_ save__bsync_beamline.experiments _item_description.description ; A description of the experiments which can be performed on this beamline. ; _item.name '_bsync_beamline.experiments' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text _item_examples.case ; MAD ; save_ save__bsync_beamline.operational _item_description.description ; Beamtime is available to the general user. ; _item.name '_bsync_beamline.operational' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'yes' ; no, beamline is being commisioned ; save_ save__bsync_beamline.general_user _item_description.description ; Percentage of beamtime available to general user. ; _item.name '_bsync_beamline.general_user' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text loop_ _item_examples.case '25' save_ save__bsync_beamline.schedule_URL _item_description.description ; Website with current beamline operating schedule ; _item.name '_bsync_beamline.schedule_URL' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'http://www.x8c.nsls.bnl.gov/schedule.html' save_ save__bsync_beamline.owner _item_description.description ; The name of the owners of the beamline. ; _item.name '_bsync_beamline.owner' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text _item_examples.case ; SBC-CAT ; save_ save__bsync_beamline.owner_url _item_description.description ; The url for the website of the owner of the beamline. ; _item.name '_bsync_beamline.owner_url' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text _item_examples.case ; http://www.sbc.anl.gov/ ; save_ save__bsync_beamline.url _item_description.description ; The url for the beamline website. ; _item.name '_bsync_beamline.url' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text _item_examples.case ; http://www.sbc.anl.gov/Facilities/beamline_19-ID.html ; save_ save__bsync_beamline.details _item_description.description ; A description of special aspects of the beamline. ; _item.name '_bsync_beamline.details' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_beamline.description _item_description.description ; A description of the beamline. ; _item.name '_bsync_beamline.description' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_beamline.template _item_description.description ; A description of the beamline template. ; _item.name '_bsync_beamline.template' _item.category_id bsync_beamline _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ ########################### ## BSYNC_DIFFRN_DETECTOR ## ########################### save_bsync_diffrn_detector _category.description ; Data items in the DETECTORS category describe the detector to measure the scattered radiation, including any analyser and post-sample collimation. ; _category.id bsync_diffrn_detector _category.mandatory_code no _category_key.name '_bsync_diffrn_detector.beamline_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_diffrn_detector.beamline_id 1 _bsync_diffrn_detector.beamline_name 'd1' _bsync_diffrn_detector.detector 'multiwire' _bsync_diffrn_detector.type 'Siemens' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_diffrn_detector.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_diffrn_detector.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_diffrn_detector.beamline_name _item_description.description ; This is a short beamline identifier. ; _item.name '_bsync_diffrn_detector.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_diffrn_detector.detector _item_description.description ; The general class of the radiation detector. ; _item.name '_bsync_diffrn_detector.detector' _item.category_id bsync_diffrn_detector _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_diffrn_detector.detector' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 loop_ _item_examples.case 'photographic film' 'scintillation counter' 'CCD plate' 'BF~3~ counter' save_ save__bsync_diffrn_detector.type _item_description.description ; The make, model or name of the detector device used. ; _item.name '_bsync_diffrn_detector.type' _item.category_id bsync_diffrn_detector _item.mandatory_code no loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_detector_type' cif_core.dic 2.0.1 '_diffrn_detector.type' cif_mm.dic 2.0.03 _item_type.code text save_ save__bsync_diffrn_detector.details _item_description.description ; A description of special aspects of the radiation detector. ; _item.name '_bsync_diffrn_detector.details' _item.category_id bsync_diffrn_detector _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_diffrn_detector.detector' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 _item_examples.case ; Need new example here. ; save_ ############################## ## BSYNC_DIFFRN_MEASUREMENT ## ############################## save_bsync_diffrn_measurement _category.description ; Data items in the MEASUREMENT category record details about data measurement and the manner in which the diffraction data are measured. ; _category.id bsync_diffrn_measurement _category.mandatory_code no loop_ _category_key.name '_bsync_diffrn_measurement.beamline_id' '_bsync_diffrn_measurement.device' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_diffrn_measurement.beamline_id 1 _bsync_diffrn_measurement.beamline_name 'bxk1' _bsync_diffrn_measurement.device '3-circle camera' _bsync_diffrn_measurement.device_type 'Supper model x' _bsync_diffrn_measurement.method 'omega scan' _bsync_diffrn_measurement.device_details ; detector distance 12 cm ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_diffrn_measurement.beamline_name _item_description.description ; This data item is a short identifier for the beamline. ; _item.name '_bsync_diffrn_measurement.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_diffrn_measurement.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_diffrn_measurement.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_diffrn_measurement.device _item_description.description ; The general class of goniometer or device used to support and orient the specimen. ; _item.name '_bsync_diffrn_measurement.device' _item.category_id bsync_diffrn_measurement _item.mandatory_code yes _item_type.code text _item_aliases.alias_name '_diffrn_measurement.device' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 loop_ _item_examples.case '3-circle camera' '4-circle camera' 'kappa-geometry camera' 'oscillation camera' 'precession camera' save_ save__bsync_diffrn_measurement.device_details _item_description.description ; A description of special aspects of the device used to measure the diffraction intensities. ; _item.name '_bsync_diffrn_measurement.device_details' _item.category_id bsync_diffrn_measurement _item.mandatory_code no loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_measurement_device_details' cif_core.dic 2.0.1 '_diffrn_measurement_device_details' cif_mm.dic 2.0.03 _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_diffrn_measurement.device_type _item_description.description ; The make, model or name of the measurement device (goniometer) used. ; _item.name '_bsync_diffrn_measurement.device_type' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_diffrn_measurement.device_type' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 loop_ _item_examples.case 'Supper model q' 'Huber model r' 'Enraf-Nonius model s' 'homemade' save_ save__bsync_diffrn_measurement.method _item_description.description ; Method used to measure intensities. ; _item.name '_bsync_diffrn_measurement.method' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement.method' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 _item_type.code text _item_examples.case 'profile data from theta/2theta scans' save_ save__bsync_diffrn_measurement.device_pinlength _item_description.description ; The range of pin lengths. ; _item.name '_bsync_diffrn_measurement.device_pinlength' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_type.code text _item_examples.case ; total height of mounting pin (or capillary) and goniometer head should be between 53 mm and 63 mm ; save_ save__bsync_diffrn_measurement.restrictions _item_description.description ; Restrictions due to possible collision. ; _item.name '_bsync_diffrn_measurement.restrictions' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_type.code text _item_examples.case ; omega: +/-25 (depends on detector distance), chi +/-95, phi no limits. ; save_ save__bsync_diffrn_measurement.distance _item_description.description ; The range of crystal to detector distances. ; _item.name '_bsync_diffrn_measurement.distance' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_type.code text _item_examples.case ; 50-1000 mm ; save_ save__bsync_diffrn_measurement.twotheta _item_description.description ; 2theta range ; _item.name '_bsync_diffrn_measurement.twotheta' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_type.code text _item_examples.case ; vertical movement of -5 to 35 ; save_ save__bsync_diffrn_measurement.cryo _item_description.description ; Cryo capability ; _item.name '_bsync_diffrn_measurement.cryo' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_type.code text _item_examples.case ; Oxford Instruments Cryojet ; save_ save__bsync_diffrn_measurement.special_capabilities _item_description.description ; Capabilities for special data collection. ; _item.name '_bsync_diffrn_measurement.special_capabilities' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_type.code text _item_examples.case ; Facilities for measurement at S K/Cl K edge region for biological samples. ; save_ save__bsync_diffrn_measurement.other_instrumentation _item_description.description ; Additional instrumentation available for use during data collection. ; _item.name '_bsync_diffrn_measurement.other_instrumentation' _item.category_id bsync_diffrn_measurement _item.mandatory_code no _item_type.code text _item_examples.case ; Motorized optical rail, slits, sample alignment stages, grazing incidence instrument. ; save_ ############################ ## BSYNC_DIFFRN_RADIATION ## ############################ save_bsync_diffrn_radiation _category.description ; Data items in the RADIATION category describe the radiation used in measuring diffraction intensities, its collimation and monochromatisation before the sample. ; _category.id bsync_diffrn_radiation _category.mandatory_code no loop_ _category_key.name '_bsync_diffrn_radiation.beamline_id' '_bsync_diffrn_radiation.monochromator' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _bsync_diffrn_radiation.beamline_id 1 _bsync_diffrn_radiation.beamline_name 'b1' _bsync_diffrn_radiation.collimation '0.3 mm double pinhole' _bsync_diffrn_radiation.monochromator 'graphite' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_diffrn_radiation.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_diffrn_radiation.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_diffrn_radiation.beamline_name _item_description.description ; This data item is a short identifier for the beamline. ; _item.name '_bsync_diffrn_radiation.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_diffrn_radiation.optics _item_description.description ; a general description of the optics including collimation and monochromator. ; _item.name '_bsync_diffrn_radiation.optics' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; 2-crystal monochromator, Si111, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing ; save_ save__bsync_diffrn_radiation.flux _item_description.description ; Flux definition needed ; _item.name '_bsync_diffrn_radiation.flux' _item.category_id bsync_diffrn_radiation _item.mandatory_code no loop_ _item_type.code text loop_ _item_examples.case ; 1x10E(10) p/s through 0.2 mm aperture ; save_ save__bsync_diffrn_radiation.flux_details _item_description.description ; Additional details about radiation flux. ; _item.name '_bsync_diffrn_radiation.flux_details' _item.category_id bsync_diffrn_radiation _item.mandatory_code no loop_ _item_type.code text save_ save__bsync_diffrn_radiation.resolving_power _item_description.description ; Resolving power of ... ; _item.name '_bsync_diffrn_radiation.resolving_power' _item.category_id bsync_diffrn_radiation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float ### _item_units.code ??? save_ save__bsync_diffrn_radiation.wavelength_range _item_description.description ; The range of wavelength in angstroms. ; _item.name '_bsync_diffrn_radiation.wavelength_range' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_type.code text save_ save__bsync_diffrn_radiation.wavelength_details _item_description.description ; Additional details about the wavelength ; _item.name '_bsync_diffrn_radiation.wavelength_details' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_type.code text save_ save__bsync_diffrn_radiation.wavelength_max _item_description.description ; The maximum radiation wavelength in angstroms or zero if single wavelength. ; _item.name '_bsync_diffrn_radiation.wavelength_max' _item.category_id bsync_diffrn_radiation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__bsync_diffrn_radiation.wavelength_min _item_description.description ; The minimum radiation wavelength in angstroms or the radiation wavelength if a single wavelength. ; _item.name '_bsync_diffrn_radiation.wavelength_min' _item.category_id bsync_diffrn_radiation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__bsync_diffrn_radiation.collimation _item_description.description ; The collimation or focusing applied to the radiation. ; _item.name '_bsync_diffrn_radiation.collimation' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_diffrn_radiation.collimation' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 loop_ _item_examples.case '0.3 mm double-pinhole' '0.5 mm' 'focusing mirrors' save_ save__bsync_diffrn_radiation.filter_edge _item_description.description ; Absorption edge in angstroms of the radiation filter used. ; _item.name '_bsync_diffrn_radiation.filter_edge' _item.category_id bsync_diffrn_radiation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_aliases.alias_name '_diffrn_radiation.filter_edge' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 _item_units.code angstroms save_ save__bsync_diffrn_radiation.inhomogeneity _item_description.description ; Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. ; _item.name '_bsync_diffrn_radiation.inhomogeneity' _item.category_id bsync_diffrn_radiation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres _item_aliases.alias_name '_diffrn_radiation.inhomogeneity' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 save_ save__bsync_diffrn_radiation.monochromator _item_description.description ; The method used to obtain monochromatic radiation. If a mono- chromator crystal is used the material and the indices of the Bragg reflection are specified. ; _item.name '_bsync_diffrn_radiation.monochromator' _item.category_id bsync_diffrn_radiation _item.mandatory_code yes _item_aliases.alias_name '_diffrn_radiation.monochromator' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 _item_type.code text loop_ _item_examples.case 'Zr filter' 'Ge 220' 'none' 'equatorial mounted graphite' save_ save__bsync_diffrn_radiation.monochromator_crystal _item_description.description ; The type of crystal(s) in the monochromator The indices of the Bragg reflection used for the filtering is specified. ; _item.name '_bsync_diffrn_radiation.monochromator_crystal' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_type.code text _item_examples.case ; Si(111) or W/B4C multilayers, water cooled. ; save_ save__bsync_diffrn_radiation.mirrors _item_description.description ; A system of optical mirrors used to focus the incident beam as it leaves the source ; _item.name '_bsync_diffrn_radiation.mirrors' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_type.code text _item_examples.case ; bent cylinder, Pt-coated Si (1:1 demagnifcation) ; save_ save__bsync_diffrn_radiation.mirror_cutoff _item_description.description ; The energy cuttoff (KeV) for the mirror system. ; _item.name '_bsync_diffrn_radiation.mirror_cutoff' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_type.code float _item_units.code KeV _item_examples.case ; 11.25 ; save_ save__bsync_diffrn_radiation.probe _item_description.description ; Name of the type of radiation used. It is strongly encouraged that this field be specified so that the probe radiation can be simply determined. ; _item.name '_bsync_diffrn_radiation.probe' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation.probe' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 _item_type.code line loop_ _item_enumeration.value 'x-ray' 'neutron' 'electron' 'gamma' save_ save__bsync_diffrn_radiation.divergence _item_description.description ; Divergence definition needed. ; _item.name '_bsync_diffrn_radiation.divergence' _item.category_id bsync_diffrn_radiation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float ## _item_units.code ? save_ save__bsync_diffrn_radiation.energy_range _item_description.description ; Energy range. ; _item.name '_bsync_diffrn_radiation.energy_range' _item.category_id bsync_diffrn_radiation _item.mandatory_code no _item_type.code text save_ ######################### ## BSYNC_DIFFRN_SOURCE ## ######################### save_bsync_diffrn_source _category.description ; Data items in the SOURCE category record details of the source of radiation. ; _category.id bsync_diffrn_source _category.mandatory_code no loop_ _category_key.name '_bsync_diffrn_source.beamline_id' '_bsync_diffrn_source.type' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 ; ; _bsync_diffrn_source.beamline_id 1 _bsync_diffrn_source.beamline_name 's1' _bsync_diffrn_source.source 'rotating anode' _bsync_diffrn_source.type 'Rigaku RU-200' _bsync_diffrn_source.power '50 kw, 180 mA' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_diffrn_source.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_diffrn_source.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_diffrn_source.beamline_name _item_description.description ; This data item is a short identifier for the beamline. ; _item.name '_bsync_diffrn_source.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_diffrn_source.beam_lifetime _item_description.description ; average beam lifetime ; _item.name '_bsync_diffrn_source.beam_lifetime' _item.category_id bsync_diffrn_source _item.mandatory_code no _item_type.code text _item_examples.case ; 40 hrs (75 mA average over 24 hr fill period) ; save_ save__bsync_diffrn_source.current _item_description.description ; The current in milliamperes at which the radiation source was operated. ; _item.name '_bsync_diffrn_source.current' _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_diffrn_source.current' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 _item_units.code milliamperes save_ save__bsync_diffrn_source.details _item_description.description ; A description of special aspects of the radiation source used. ; _item.name '_bsync_diffrn_source.details' _item.category_id bsync_diffrn_source _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_diffrn_source.details' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 save_ save__bsync_diffrn_source.power _item_description.description ; The power in kilowatts at which the radiation source was operated. ; _item.name '_bsync_diffrn_source.power' _item.category_id bsync_diffrn_source _item.mandatory_code no _item_type.code float _item_units.code kilowatts _item_aliases.alias_name '_diffrn_source.power' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 save_ save__bsync_diffrn_source.size _item_description.description ; The dimensions of the source as viewed from the sample. ; _item.name '_bsync_diffrn_source.size' _item.category_id bsync_diffrn_source _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_diffrn_source.size' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 loop_ _item_examples.case '8mm x 0.4 mm fine-focus' save_ save__bsync_diffrn_source.source _item_description.description ; The general class of the radiation source. ; _item.name '_bsync_diffrn_source.source' _item.category_id bsync_diffrn_source _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'undulator' 'bending magnet' 'wiggler' save_ save__bsync_diffrn_source.type _item_description.description ; The make, model or name of the source of radiation. ; _item.name '_bsync_diffrn_source.type' _item.category_id bsync_diffrn_source _item.mandatory_code yes _item_type.code text loop_ _item_linked.parent_name _item_linked.child_name '_bsync_diffrn_source.type' '_bsync_beamline.source_type' _item_aliases.alias_name '_diffrn_source.type' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 loop_ _item_examples.case 'NSLS beamline X8C' 'Rigaku RU200' save_ save__bsync_diffrn_source.voltage _item_description.description ; The voltage in kilovolts at which the radiation source was operated. ; _item.name '_bsync_diffrn_source.voltage' _item.category_id bsync_diffrn_source _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_diffrn_source.voltage' _item_aliases.dictionary cif_mm.dic _item_aliases.version 2.0.03 _item_units.code kilovolts save_ ####################### ## BSYNC_DIFFRN_LAB ## ####################### save_bsync_diffrn_lab _category.description ; Data items in the LAB category describe the laboratory facilities and biohazard capabilities at the beamline ; _category.id bsync_diffrn_lab _category.mandatory_code no _category_key.name '_bsync_diffrn_lab.beamline_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_diffrn_lab.beamline_id 1 _bsync_diffrn_lab.beamline_name 'A1' _bsync_diffrn_lab.lab_facilities 'cold room and biochemistry' _bsync_diffrn_lab.biohazard 'P2' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_diffrn_lab.beamline_name _item_description.description ; This is a short beamline identifier. ; _item.name '_bsync_diffrn_lab.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_diffrn_lab.name _item_description.description ; Lab name. ; _item.name '_bsync_diffrn_lab.name' _item.mandatory_code yes _item_type.code text save_ save__bsync_diffrn_lab.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_diffrn_lab.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_diffrn_lab.lab_facilities _item_description.description ; Lab Facilities at the beamline. ; _item.name '_bsync_diffrn_lab.lab_facilities' _item.category_id bsync_diffrn_lab _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_diffrn_lab.biohazard _item_description.description ; Biohazard level allowed at the beamline ; _item.name '_bsync_diffrn_lab.biohazard' _item.category_id bsync_diffrn_lab _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ #################### ## BSYNC_HARDWARE ## #################### save_bsync_hardware _category.description ; Data items in the HARDWARE category record details about the hardware available for data collection and structure determination and for data back-up. ; _category.id bsync_hardware _category.mandatory_code no loop_ _category_key.name '_bsync_hardware.beamline_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_hardware.beamline_id 1 _bsync_hardware.backup 'FireWire and USB disk drives' ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__bsync_hardware.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_hardware.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_hardware.beamline_name _item_description.description ; This data item is a short identifier for the beamline. ; _item.name '_bsync_hardware.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_hardware.name _item_description.description ; The name of the hardware. ; _item.name '_bsync_hardware.name' _item.category_id bsync_hardware _item.mandatory_code no _item_type.code text save_ save__bsync_hardware.backup _item_description.description ; Backup hardware. ; _item.name '_bsync_hardware.backup' _item.category_id bsync_hardware _item.mandatory_code no _item_type.code text save_ #################### ## BSYNC_SOFTWARE ## #################### save_bsync_software _category.description ; Data items in the SOFTWARE category record details about the software available for data collection and structure determination. ; _category.id bsync_software _category.mandatory_code no loop_ _category_key.name '_bsync_software.beamline_id' '_bsync_software.name' '_bsync_software.version' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _bsync_software.beamline_id _bsync_software.name _bsync_software.version _bsync_software.date _bsync_software.type _bsync_software.contact_author _bsync_software.contact_author_email _bsync_software.location _bsync_software.classification _bsync_software.language _bsync_software.compiler_name _bsync_software.compiler_version _bsync_software.hardware _bsync_software.os _bsync_software.os_version _bsync_software.dependencies _bsync_software.mods _bsync_software.description Prolsq unknown . program 'Wayne A. Hendrickson' ? 'ftp://rosebud.sdsc.edu/pub/sdsc/xtal/CCP4/ccp4/' refinement ref5 Fortran 'Convex Fortran' v8.0 'Convex C220' ConvexOS v10.1 'Requires that Protin be run first' optimized 'restrained least-squares refinement' ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__bsync_software.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_software.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_software.beamline_name _item_description.description ; This data item is a short identifier for the beamline. ; _item.name '_bsync_software.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_software.classification _item_description.description ; The classification of the program according to its major function. ; _item.name '_bsync_software.classification' _item.category_id bsync_software _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value 'data collection' 'data reduction' 'phasing' 'model building' 'refinement' 'validation' 'other' save_ save__bsync_software.compiler_name _item_description.description ; The compiler used to compile the software. ; _item.name '_bsync_software.compiler_name' _item.category_id bsync_software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Convex Fortran' 'gcc' 'DEC C' save_ save__bsync_software.compiler_version _item_description.description ; The version of the compiler used to compile the software. ; _item.name '_bsync_software.compiler_version' _item.category_id bsync_software _item.mandatory_code no _item_type.code line loop_ _item_examples.case '3.1' '2.1 alpha' save_ save__bsync_software.contact_author _item_description.description ; The recognized contact author of the software. This could be the original author, modifier of the code, or maintainer, but should be the individual most commonly associated with the code. ; _item.name '_bsync_software.contact_author' _item.category_id bsync_software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'T. Alwyn Jones' 'Axel Brunger' save_ save__bsync_software.contact_author_email _item_description.description ; The email address of the _bsync_software.contact_author. ; _item.name '_bsync_software.contact_author_email' _item.category_id bsync_software _item.mandatory_code no _item_type.code line _item_examples.case 'bourne@sdsc.edu' save_ save__bsync_software.date _item_description.description ; The date the software was released. ; _item.name '_bsync_software.date' _item.category_id bsync_software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 1991-10-01 1990-04-30 save_ save__bsync_software.description _item_description.description ; Description of the software. ; _item.name '_bsync_software.description' _item.category_id bsync_software _item.mandatory_code no _item_type.code line _item_examples.case 'Uses method of restrained least squares' save_ save__bsync_software.dependencies _item_description.description ; Any prerequisite software required to run _bsync_software.name. ; _item.name '_bsync_software.dependencies' _item.category_id bsync_software _item.mandatory_code no _item_type.code line _item_examples.case 'PDBlib class library' save_ save__bsync_software.hardware _item_description.description ; The hardware upon which the software was run. ; _item.name '_bsync_software.hardware' _item.category_id bsync_software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Sun Sparc 10 model 41' 'Dec Alpha 3000 model 500S' 'Silicon Graphics Elan' 'Compaq PC 486/66' save_ save__bsync_software.language _item_description.description ; The major computing language in which the software is coded. ; _item.name '_bsync_software.language' _item.category_id bsync_software _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value Ada assembler Awk Basic 'C++' C csh Fortran Java ksh Pascal Perl Python sh Tcl Other save_ save__bsync_software.location _item_description.description ; An Internet address in the form of a URL describing where details of the software can be found. ; _item.name '_bsync_software.location' _item.category_id bsync_software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'http://rosebud.sdsc.edu/projects/pb/IUCr/software.html' 'ftp://ftp.sdsc.edu/pub/sdsc/biology/' save_ save__bsync_software.mods _item_description.description ; Any noteworthy modifications to the base software, if applicable. ; _item.name '_bsync_software.mods' _item.category_id bsync_software _item.mandatory_code no _item_type.code line _item_examples.case 'Added support for space group F432' save_ save__bsync_software.name _item_description.description ; The name of the software. ; _item.name '_bsync_software.name' _item.category_id bsync_software _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'Merlot' 'O' 'Xengen' 'X-plor' save_ save__bsync_software.os _item_description.description ; The name of the operating system under which the software runs. ; _item.name '_bsync_software.os' _item.category_id bsync_software _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Ultrix' 'OpenVMS' 'DOS' 'Windows 95' 'Windows NT' 'Irix' 'HPUX' 'DEC Unix' save_ save__bsync_software.os_version _item_description.description ; The version of the operating system under which the software runs. ; _item.name '_bsync_software.os_version' _item.category_id bsync_software _item.mandatory_code no _item_type.code text loop_ _item_examples.case '3.1' '4.2.1' save_ save__bsync_software.type _item_description.description ; The classification of the software according to the most common types. ; _item.name '_bsync_software.type' _item.category_id bsync_software _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value _item_enumeration.detail program ; individual program with limited functionality ; library ; used by a program at load time ; package ; collections of programs with multiple functionality ; filter ; filters input and output streams ; jiffy ; short simple program ; other ; all other classifications ; save_ save__bsync_software.version _item_description.description ; The version of the software. ; _item.name '_bsync_software.version' _item.category_id bsync_software _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'v1.0' 'beta' '3.1-2' 'unknown' save_ ########################## ## BSYNC_ADMIN_CONTACT ## ########################## save_bsync_admin_contact _category.description ; Data items in the BSYNC_ADMIN_CONTACT category describe the adiministrative, logistical, contact and travel infomtion in preparing a trip to a synchrotron. ; _category.id bsync_admin_contact _category.mandatory_code no _category_key.name '_bsync_admin_contact.beamline_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_admin_contact.beamline_id 1 _bsync_admin_contact.beamline_name 'd1' _bsync_admin_contact.for_technical_name 'Joe Smith' _bsync_admin_contact.for_technical_email 'smith@synchrotron.edu' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_admin_contact.beamline_name _item_description.description ; This is a short beamline identifier. ; _item.name '_bsync_admin_contact.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_admin_contact.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_admin_contact.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_admin_contact.website _item_description.description ; Website with staff contacts. ; _item.name '_bsync_admin_contact.website' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_contact.for_technical_name _item_description.description ; Name of beamline contact person for technical information. ; _item.name '_bsync_admin_contact.for_technical_name' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_contact.for_beamtime_name _item_description.description ; Name of contact person for proposal information ; _item.name '_bsync_admin_contact.for_beamtime_name' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_contact.for_technical_phone _item_description.description ; Phone number of beamline contact person. ; _item.name '_bsync_admin_contact.for_technical_phone' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_contact.for_beamtime_phone _item_description.description ; Phone number of beamline contact person. ; _item.name '_bsync_admin_contact.for_beamtime_phone' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_contact.for_technical_email _item_description.description ; Email of beamline contact person. ; _item.name '_bsync_admin_contact.for_technical_email' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_contact.for_beamtime_email _item_description.description ; Email of beamline contact person. ; _item.name '_bsync_admin_contact.for_beamtime_email' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_contact.shipping_address _item_description.description ; The shipping address of beamline facilities. ; _item.name '_bsync_admin_contact.shipping_address' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_contact.contact_address _item_description.description ; Address of beamline contact person. ; _item.name '_bsync_admin_contact.contact_address' _item.category_id bsync_admin_contact _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ ######################### ## BSYNC_ADMIN_LOGOS ## ######################### save_bsync_admin_logos _category.description ; Data items in the BSYNC_ADMIN_LOGOS category describe the logo associated with each beamline and synchrotron. ; _category.id bsync_admin_logos _category.mandatory_code no loop_ _category_key.name '_bsync_admin_logos.beamline_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 ; ; _bsync_admin_logos.beamline_id 1 _bsync_admin_logos.crystallography 'hbar_pxssrl.gif' _bsync_admin_logos.synchrotron 'hbar_ssrl.gif' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_admin_logos.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_admin_logos.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_admin_logos.beamline_name _item_description.description ; This data item is a short identifier for the beamline. ; _item.name '_bsync_admin_logos.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_admin_logos.crystallography _item_description.description ; The logo for the cat or prt or crystallography group that operates the beamline. ; _item.name '_bsync_admin_logos.crystallography' _item.category_id bsync_admin_logos _item.mandatory_code no _item_type.code text _item_examples.case 'hbar_pxssrl.gif' save_ save__bsync_admin_logos.synchrotron _item_description.description ; The logo for the synchrotron facility ; _item.name '_bsync_admin_logos.synchrotron' _item.category_id bsync_admin_logos _item.mandatory_code no _item_type.code text _item_examples.case 'hbar_ssrl.gif' save_ ############################### ## BSYNC_ADMIN_APPLICATIONS ## ############################### save_bsync_admin_applications _category.description ; Data items in the APPLICATIONS category describe the application procedure to obtain beamtime at a given beamline. ; _category.id bsync_admin_applications _category.mandatory_code no _category_key.name '_bsync_admin_applications.beamline_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_admin_applications.beamline_id 1 _bsync_admin_applications.beamline_name 'd1' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_admin_applications.beamline_name _item_description.description ; This is a short beamline identifier. ; _item.name '_bsync_admin_applications.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_admin_applications.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_admin_applications.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_admin_applications.url _item_description.description ; url for applications. ; _item.name '_bsync_admin_applications.url' _item.category_id bsync_admin_applications _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_applications.url_name _item_description.description ; name of the url for applications. ; _item.name '_bsync_admin_applications.url_name' _item.category_id bsync_admin_applications _item.mandatory_code no _item_type.code text _item_examples.case ; Procedure for obtaining Beam Time ; save_ save__bsync_admin_applications.deadlines _item_description.description ; deadline for beamtime applications ; _item.name '_bsync_admin_applications.deadlines' _item.category_id bsync_admin_applications _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_applications.procedure _item_description.description ; procedure for applications ; _item.name '_bsync_admin_applications.procedure' _item.category_id bsync_admin_applications _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ ############################ ## BSYNC_FACILITY_WEBSITE ## ############################ save_bsync_facility_website _category.description ; Data items in the BSYNC_FACILITY_WEBSITE category record details about hyperlinks and desciptions of those links to the synchrotron facility website. This category forms the basis of the BioSync Web portal. ; _category.id bsync_facility_website _category.mandatory_code no loop_ _category_key.name '_bsync_facility_website.facility_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - SSRL ; ; _bsync_facility_website.facility_id ssrl _bsync_facility_website.facility_map_url 'http://www-ssrl.slac.stanford.edu/welcome.html' ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__bsync_facility_website.facility_id _item_description.description ; This data item is a pointer to _bsync_facility.id in the BSYNC_FACILITY category. ; _item.name '_bsync_facility_website.facility_id' _item.mandatory_code yes _item_type.code code save_ save__bsync_facility_website.ring_status_url _item_description.description ; The url for the current ring status ; _item.name '_bsync_facility_website.ring_status_url' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.ring_status _item_description.description ; A description of the url for the current ring status ; _item.name '_bsync_facility_website.ring_status' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.facility_map_url _item_description.description ; The url for a map of the synchrotron facility ; _item.name '_bsync_facility_website.facility_map_url' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.facility_map _item_description.description ; A description of the url for the facility map ; _item.name '_bsync_facility_website.facility_map' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.directions_url _item_description.description ; The url for directions to the facility ; _item.name '_bsync_facility_website.directions_url' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.directions _item_description.description ; A description of the url for directions to the facility ; _item.name '_bsync_facility_website.directions' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.accomodation_url _item_description.description ; The url for accomodations at the facility ; _item.name '_bsync_facility_website.accomodation_url' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.accomodation _item_description.description ; A description of the url for accomodations at the facility ; _item.name '_bsync_facility_website.accomodation' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.publications_url _item_description.description ; The url for crystallography publications from research at the facility ; _item.name '_bsync_facility_website.publications_url' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.publications _item_description.description ; A description of the url for crystallography publications from research at the facility ; _item.name '_bsync_facility_website.publications' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.operation_schedule_url _item_description.description ; The url for long term operation of the facility ; _item.name '_bsync_facility_website.operation_schedule_url' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.operation_schedule _item_description.description ; A description of the url for long term operation of the facility ; _item.name '_bsync_facility_website.operation_schedule' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.safety_training_url _item_description.description ; The url for info. on safety training at the facility ; _item.name '_bsync_facility_website.safety_training_url' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ save__bsync_facility_website.safety_training _item_description.description ; A description of safety training at the facility ; _item.name '_bsync_facility_website.safety_training' _item.category_id bsync_facility_website _item.mandatory_code no _item_type.code text save_ ############################ ## BSYNC_ADMIN_SCHEDULES ## ############################ save_bsync_admin_schedules _category.description ; Data items in the SCHEDULES category describe the application procedure to obtain beamtime at a given beamline. ; _category.id bsync_admin_schedules _category.mandatory_code no _category_key.name '_bsync_admin_schedules.beamline_id' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _bsync_admin_schedules.beamline_id 1 _bsync_admin_schedules.beamline_name 'd1' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__bsync_admin_schedules.beamline_name _item_description.description ; This is a short beamline identifier. ; _item.name '_bsync_admin_schedules.beamline_name' _item.mandatory_code yes _item_type.code code save_ save__bsync_admin_schedules.beamline_id _item_description.description ; This data item is a pointer to _bsync_beamline.id in the BSYNC_BEAMLINE category. ; _item.name '_bsync_admin_schedules.beamline_id' _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 save_ save__bsync_admin_schedules.long_term _item_description.description ; long term operating schedule for the synchrotron. ; _item.name '_bsync_admin_schedules.long_term' _item.category_id bsync_admin_schedules _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ save__bsync_admin_schedules.ring_status _item_description.description ; current ring status ; _item.name '_bsync_admin_schedules.ring_status' _item.category_id bsync_admin_schedules _item.mandatory_code no _item_type.code text _item_examples.case ; Procedure for obtaining Beam Time ; save_ save__bsync_admin_schedules.beamline _item_description.description ; beamline schedules ; _item.name '_bsync_admin_schedules.beamline' _item.category_id bsync_admin_schedules _item.mandatory_code no _item_type.code text _item_examples.case ; Need new example here. ; save_ ################# ## BSYNC_LINKS ## ################# save_bsync_links _category.description ; Data items in the BSYNC_LINKS category record details about hyperlinks and desciptions of those links to the synchrotron facility website. This category forms the basis of the BioSync Web portal. ; _category.id bsync_links _category.mandatory_code no loop_ _category_key.name '_bsync_links.facility_id' '_bsync_links.name' loop_ _category_group.id 'inclusive_group' 'bsync_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - SSRL ; ; _bsync_links.facility_id ssrl _bsync_links.name ;Stanford Synchrotron Radiation Laboratory (SSRL) ; _bsync_links.url 'http://www-ssrl.slac.stanford.edu/welcome.html' _bsync_links.description 'welcome page for all beamlines' ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__bsync_links.facility_id _item_description.description ; This data item is a pointer to _bsync_facility.id in the BSYNC_FACILITY category. ; _item.name '_bsync_links.facility_id' _item.mandatory_code yes _item_type.code code save_ save__bsync_links.name _item_description.description ; Site name for the link. ; _item.name '_bsync_links.name' _item.category_id bsync_links _item.mandatory_code yes _item_type.code text save_ save__bsync_links.category _item_description.description ; The category for the link based on the BioSync Web site, contacts, travel, publications, schedules ; _item.name '_bsync_links.category' _item.category_id bsync_links _item.mandatory_code no _item_type.code text loop_ _item_enumeration.value 'Travel' 'Publications' 'Calendars' 'Training' 'Beam time' 'Maps' 'Operations' 'Staff' 'Synchrotron and Crystallography Orgs' 'Synchrotron and Organizations' 'General Information' 'Shipping' 'Beam time, xtal beamlines' 'Beam time, other beamlines' 'Beam time, X-ray absorption spectrocopy' 'Beam Time - crystallography' 'Beam Time - saxs & xas' save_ save__bsync_links.url _item_description.description ; Site location (URL) for the link ; _item.name '_bsync_links.url' _item.category_id bsync_links _item.mandatory_code no _item_type.code text save_ save__bsync_links.description _item_description.description ; A description of the website ; _item.name '_bsync_links.description' _item.category_id bsync_links _item.mandatory_code no _item_type.code text save_ ## ## End of file - mmcif_biosync_def-1.dic ## # loop_ _pdbx_item_linked_group.category_id _pdbx_item_linked_group.link_group_id _pdbx_item_linked_group.label _pdbx_item_linked_group.context _pdbx_item_linked_group.condition_id bsync_beamline 1 bsync_beamline:bsync_diffrn_source:1 . . bsync_beamline 2 bsync_beamline:bsync_facility:2 . . bsync_diffrn_detector 1 bsync_diffrn_detector:bsync_beamline:1 . . bsync_diffrn_measurement 1 bsync_diffrn_measurement:bsync_beamline:1 . . bsync_diffrn_radiation 1 bsync_diffrn_radiation:bsync_beamline:1 . . bsync_diffrn_source 1 bsync_diffrn_source:bsync_beamline:1 . . bsync_facility_website 1 bsync_facility_website:bsync_facility:1 . . bsync_software 1 bsync_software:bsync_beamline:1 . . # loop_ _pdbx_item_linked_group_list.child_category_id _pdbx_item_linked_group_list.link_group_id _pdbx_item_linked_group_list.child_name _pdbx_item_linked_group_list.parent_name _pdbx_item_linked_group_list.parent_category_id bsync_beamline 1 '_bsync_beamline.source_type' '_bsync_diffrn_source.type' bsync_diffrn_source bsync_beamline 2 '_bsync_beamline.facility_id' '_bsync_facility.id' bsync_facility bsync_diffrn_detector 1 '_bsync_diffrn_detector.beamline_id' '_bsync_beamline.id' bsync_beamline bsync_diffrn_measurement 1 '_bsync_diffrn_measurement.beamline_id' '_bsync_beamline.id' bsync_beamline bsync_diffrn_radiation 1 '_bsync_diffrn_radiation.beamline_id' '_bsync_beamline.id' bsync_beamline bsync_diffrn_source 1 '_bsync_diffrn_source.beamline_id' '_bsync_beamline.id' bsync_beamline bsync_facility_website 1 '_bsync_facility_website.facility_id' '_bsync_facility.id' bsync_facility bsync_software 1 '_bsync_software.beamline_id' '_bsync_beamline.id' bsync_beamline #