From jawahar@ebi.ac.uk Mon Aug 1 13:26:09 2005 Date: Mon, 01 Aug 2005 11:43:31 +0100 From: Jawahar Swaminathan To: Kim Henrick Cc: P.J.Briggs , Martyn Winn , Peter Briggs Subject: Re: Non-standard tokens from mtz2various [ The following text is in the "ISO-8859-1" character set. ] [ Your display is set for the "US-ASCII" character set. ] [ Some characters may be displayed incorrectly. ] Dear Peter and Kim, These cif items occur quite often in the MTZ files we receive from our depositors. These items are now part of the cif exchange dictionary (mmcif_ccp4.dic) as we were in touch with John Westbrook more than two years ago in order that we could include these columns from structure factor flags rather than throwing them away. In theory, the RCSB should also be able to use this information for their processing needs, since they are now part of the standard data exchange mmCIF dictionaries. I am enclosing a copy of the mmcif_ccp4.dic file that was last updated on the 25th of July. We do use cif2mtz in order that we may run SFCHECK, but both cif2mtz and sfcheck throw away these items during analysis. It would be great if mtz2various could parse this information and write out the necessary information, when present. Hope that answers your question. best regards - Jawahar Jawahar Swaminathan, Ph.D. PDB Depositions MSD-EBI >>Hi Kim & Martyn >> >>I'm trying to unravel some issues with the tokens written out by the >>MTZ2VARIOUS program. In May 2003 Martyn modified the CIF output: >> >> >> >>The explicit anomalous columns/tokens are: >> >> _refln.ccp4_SAD_F_meas_plus_au F(+) >> _refln.ccp4_SAD_F_meas_plus_sigma_au SIGF(+) >> _refln.ccp4_SAD_F_meas_minus_au F(-) >> _refln.ccp4_SAD_F_meas_minus_sigma_au SIGF(-) >> _refln.ccp4_SAD_phase_anom DP >> _refln.ccp4_SAD_phase_anom_sigma SIGDP >> _refln.ccp4_I_plus I(+) >> _refln.ccp4_I_plus_sigma SIGI(+) >> _refln.ccp4_I_minus I(-) >> _refln.ccp4_I_minus_sigma SIGI(-) >> >>There are some problems: >> >>1. CIF2MTZ doesn't recognise these so it cannot back-transform the CIF >> output from MTZ2VARIOUS to MTZ (this is not really of interest here) >>2. The RCSB doesn't recognise these tokens and so MTZ2VARIOUS >> cannot be used to generate structure factors for deposition if >> anomalous data is present. >> >>So what I want to know is: does the EBI recognise/accept these tokens in >>deposited CIF files? or are they converted to something else, or what? >> >>Thanks for your help, best wishes >> >>Pete >> >>-- >>_____________________________________________________ >>Peter J Briggs, pjx@ccp4.ac.uk Tel: +44 1925 603826 >>CCP4, ccp4@ccp4.ac.uk Fax: +44 1925 603825 >> http://www.ccp4.ac.uk/ >>Daresbury Laboratory, Daresbury, Warrington WA4 4AD >> >> >> > >Kim HENRICK henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629 > > > [ Part 2: "Attached Text" ] ########################################################################### # # File: mmcif_ccp4.dic # Date: Mon Jul 25 18:01:19 EDT 2005 # # Created from files in CVS module dict-mmcif_ccp4.dic unless noted: # mmcif_ccp4-header.dic # mmcif_ccp4-data.dic # mmcif_ccp4-def-1.dic # ########################################################################### ########################################################################### # # File: mmcif_ccp4-header.dic # # CCP4 Extension Data Dictionary # # This dictionary supplements the contents of the mmCIF data dictionary # with additional data items required to describe the details of the # structure determination using the CCP4 program system. # # This supplement was created by Kim Henrick at Molecular Structure # Database (MSD) Group/EBI and the CCP4 development group. # # # Header Section # ############################################################################## data_mmcif_ccp4.dic _datablock.id mmcif_ccp4.dic _datablock.description ; This data block holds the CCP4 Extension Data Dictionary ; _dictionary.title mmcif_ccp4.dic _dictionary.version 1.00 _dictionary.datablock_id mmcif_ccp4.dic ######################## ## DICTIONARY_HISTORY ## ######################## loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 1.00 2001-04-18 'Initial version' ### EOF mmcif_ccp4-header.dic ########################################################################### # # File: mmcif_ccp4-data.dic # # CCP4 Extension Data Dictionary # # This dictionary supplements the contents of the mmCIF data dictionary # with additional data items required to describe the details of the # structure determination using the CCP4 program system. # # This supplement was created by Kim Henrick at Molecular Structure # Database (MSD) Group/EBI and the CCP4 development group. # # # 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 '[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words ... ; ucode uchar '[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (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. ; ##################### ## ITEM_UNITS_LIST ## ##################### loop_ _item_units_list.code _item_units_list.detail 'angstroms' 'angstroms (meters * 10^(-10))' 'angstroms_squared' 'angstroms squared (meters * 10^(-10))^2' 'degrees' 'degrees (of arc)' 'angstroms_degrees' 'angstroms x degrees' 'degrees_squared' 'degrees squared' ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description 'inclusive_group' . ; All categories ; 'refine_group' 'inclusive_group' ; Categories which pertain to refinement ; ### EOF mmcif_ccp4-data.dic########################################################################### # # File: mmcif_ccp4-header.dic # # CCP4 Extension Data Dictionary # # This dictionary supplements the contents of the mmCIF data dictionary # with additional data items required to describe the details of the # structure determination using the CCP4 program system. # # This supplement was created by Kim Henrick at Molecular Structure # Database (MSD) Group/EBI and the CCP4 development group. # # # Definition Section 1 # ############################################################################## save_ccp4_refine_tls _category.description ; Data items in the REFINE_TLS category record details about TLS parameters used in structure refinement. Note that the intention is primarily to describe directly refined TLS parameters, although other methods of obtaining TLS parameters may be covered, see item _ccp4_refine_tls.method ; _category.id ccp4_refine_tls _category.mandatory_code no loop_ _category_key.name '_ccp4_refine_tls.id' loop_ _category_group.id 'inclusive_group' 'refine_group' save_ save__ccp4_refine_tls.id _item_description.description ; The value of _ccp4_refine_tls.id must uniquely identify a record in the CCP4_REFINE_TLS list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_ccp4_refine_tls.id' _item.category_id ccp4_refine_tls _item.mandatory_code yes loop_ _item_linked.child_name _item_linked.parent_name '_ccp4_refine_tls_group.refine_tls_id' '_ccp4_refine_tls.id' _item_type.code code loop_ _item_examples.case 1 A save_ save__ccp4_refine_tls.details _item_description.description ; A description of the TLS group, such as a domain name or a chemical group name. ; _item.name '_ccp4_refine_tls.details' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Chain A catalytic domain' 'Chain A Tyr 56 side chain' save_ save__ccp4_refine_tls.method _item_description.description ; The method by which the TLS parameters were obtained. ; _item.name '_ccp4_refine_tls.method' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail refined ; TLS parameters refined directly against crystallographic residual ; fitted ; TLS parameters fitted to previously refined anisotropic displacement parameters ; save_ save__ccp4_refine_tls.origin_x _item_description.description ; The x coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in _atom_sites.Cartn_transform_axes. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.origin_x' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_dependent.dependent_name '_ccp4_refine_tls.origin_y' '_ccp4_refine_tls.origin_z' save_ save__ccp4_refine_tls.origin_y _item_description.description ; The y coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in _atom_sites.Cartn_transform_axes. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.origin_y' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_dependent.dependent_name '_ccp4_refine_tls.origin_x' '_ccp4_refine_tls.origin_z' save_ save__ccp4_refine_tls.origin_z _item_description.description ; The z coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in _atom_sites.Cartn_transform_axes. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.origin_z' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_dependent.dependent_name '_ccp4_refine_tls.origin_x' '_ccp4_refine_tls.origin_y' save_ save__ccp4_refine_tls.T[1][1] _item_description.description ; The [1][1] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.T[1][1]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[1][1]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.T[1][1]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.T[1][1]. ; _item.name '_ccp4_refine_tls.T[1][1]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[1][1]' associated_value _item_units.code angstroms_squared save_ save__ccp4_refine_tls.T[1][2] _item_description.description ; The [1][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.T[1][2]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[1][2]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.T[1][2]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.T[1][2]. ; _item.name '_ccp4_refine_tls.T[1][2]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[1][2]' associated_value _item_units.code angstroms_squared save_ save__ccp4_refine_tls.T[1][3] _item_description.description ; The [1][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.T[1][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[1][3]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.T[1][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.T[1][3]. ; _item.name '_ccp4_refine_tls.T[1][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[1][3]' associated_value _item_units.code angstroms_squared save_ save__ccp4_refine_tls.T[2][2] _item_description.description ; The [2][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.T[2][2]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[2][2]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.T[2][2]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.T[2][2]. ; _item.name '_ccp4_refine_tls.T[2][2]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[2][2]' associated_value _item_units.code angstroms_squared save_ save__ccp4_refine_tls.T[2][3] _item_description.description ; The [2][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.T[2][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[2][3]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.T[2][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.T[2][3]. ; _item.name '_ccp4_refine_tls.T[2][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[2][3]' associated_value _item_units.code angstroms_squared save_ save__ccp4_refine_tls.T[3][3] _item_description.description ; The [3][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.T[3][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[3][3]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.T[3][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.T[3][3]. ; _item.name '_ccp4_refine_tls.T[3][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.T[3][3]' associated_value _item_units.code angstroms_squared save_ save__ccp4_refine_tls.L[1][1] _item_description.description ; The [1][1] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.L[1][1]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[1][1]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.L[1][1]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.L[1][1]. ; _item.name '_ccp4_refine_tls.L[1][1]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[1][1]' associated_value _item_units.code degrees_squared save_ save__ccp4_refine_tls.L[1][2] _item_description.description ; The [1][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.L[1][2]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[1][2]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.L[1][2]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.L[1][2]. ; _item.name '_ccp4_refine_tls.L[1][2]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[1][2]' associated_value _item_units.code degrees_squared save_ save__ccp4_refine_tls.L[1][3] _item_description.description ; The [1][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.L[1][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[1][3]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.L[1][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.L[1][3]. ; _item.name '_ccp4_refine_tls.L[1][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[1][3]' associated_value _item_units.code degrees_squared save_ save__ccp4_refine_tls.L[2][2] _item_description.description ; The [2][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.L[2][2]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[2][2]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.L[2][2]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.L[2][2]. ; _item.name '_ccp4_refine_tls.L[2][2]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[2][2]' associated_value _item_units.code degrees_squared save_ save__ccp4_refine_tls.L[2][3] _item_description.description ; The [2][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.L[2][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[2][3]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.L[2][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.L[2][3]. ; _item.name '_ccp4_refine_tls.L[2][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[2][3]' associated_value _item_units.code degrees_squared save_ save__ccp4_refine_tls.L[3][3] _item_description.description ; The [3][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_ccp4_refine_tls.L[3][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[3][3]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd save_ save__ccp4_refine_tls.L[3][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.L[3][3]. ; _item.name '_ccp4_refine_tls.L[3][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.L[3][3]' associated_value _item_units.code degrees_squared save_ save__ccp4_refine_tls.S[1][1] _item_description.description ; The [1][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. ; _item.name '_ccp4_refine_tls.S[1][1]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[1][1]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[1][1]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[1][1]. ; _item.name '_ccp4_refine_tls.S[1][1]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[1][1]' associated_value _item_units.code angstroms_degrees save_ save__ccp4_refine_tls.S[1][2] _item_description.description ; The [1][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.S[1][2]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[1][2]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[1][2]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[1][2]. ; _item.name '_ccp4_refine_tls.S[1][2]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[1][2]' associated_value _item_units.code angstroms_degrees save_ save__ccp4_refine_tls.S[1][3] _item_description.description ; The [1][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.S[1][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[1][3]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[1][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[1][3]. ; _item.name '_ccp4_refine_tls.S[1][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[1][3]' associated_value _item_units.code angstroms_degrees save_ save__ccp4_refine_tls.S[2][1] _item_description.description ; The [2][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.S[2][1]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[2][1]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[2][1]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[2][1]. ; _item.name '_ccp4_refine_tls.S[2][1]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[2][1]' associated_value _item_units.code angstroms_degrees save_ save__ccp4_refine_tls.S[2][2] _item_description.description ; The [2][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. ; _item.name '_ccp4_refine_tls.S[2][2]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[2][2]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[2][2]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[2][2]. ; _item.name '_ccp4_refine_tls.S[2][2]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[2][2]' associated_value _item_units.code angstroms_degrees save_ save__ccp4_refine_tls.S[2][3] _item_description.description ; The [2][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.S[2][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[2][3]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[2][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[2][3]. ; _item.name '_ccp4_refine_tls.S[2][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[2][3]' associated_value _item_units.code angstroms_degrees save_ save__ccp4_refine_tls.S[3][1] _item_description.description ; The [3][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.S[3][1]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[3][1]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[3][1]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[3][1]. ; _item.name '_ccp4_refine_tls.S[3][1]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[3][1]' associated_value _item_units.code angstroms_degrees save_ save__ccp4_refine_tls.S[3][2] _item_description.description ; The [3][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_ccp4_refine_tls.S[3][2]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[3][2]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[3][2]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[3][2]. ; _item.name '_ccp4_refine_tls.S[3][2]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[3][2]' associated_value _item_units.code angstroms_degrees save_ save__ccp4_refine_tls.S[3][3] _item_description.description ; The [3][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. ; _item.name '_ccp4_refine_tls.S[3][3]' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[3][3]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd save_ save__ccp4_refine_tls.S[3][3]_esd _item_description.description ; The estimated standard deviation of _ccp4_refine_tls.S[3][3]. ; _item.name '_ccp4_refine_tls.S[3][3]_esd' _item.category_id ccp4_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_ccp4_refine_tls.S[3][3]' associated_value _item_units.code angstroms_degrees save_ save_ccp4_refine_tls_group _category.description ; Data items in the CCP4_REFINE_TLS_GROUP category record details about a fragment of a TLS group. Properties of the TLS group are recorded in CCP4_REFINE_TLS ; _category.id ccp4_refine_tls_group _category.mandatory_code no loop_ _category_key.name '_ccp4_refine_tls_group.id' loop_ _category_group.id 'inclusive_group' 'refine_group' save_ save__ccp4_refine_tls_group.id _item_description.description ; The value of _ccp4_refine_tls_group.id must uniquely identify a record in the REFINE_TLS_GROUP list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_ccp4_refine_tls_group.id' _item.category_id ccp4_refine_tls_group _item.mandatory_code yes _item_type.code code loop_ _item_examples.case 1 A save_ save__ccp4_refine_tls_group.refine_tls_id _item_description.description ; This data item is a pointer to _ccp4_refine_tls.id in the REFINE_TLS category. ; _item.name '_ccp4_refine_tls_group.refine_tls_id' _item.category_id ccp4_refine_tls_group _item.mandatory_code yes _item_type.code code save_ save__ccp4_refine_tls_group.beg_label_asym_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ccp4_refine_tls_group.beg_label_asym_id' _item.category_id ccp4_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_ccp4_refine_tls_group.beg_label_asym_id' '_atom_site.label_asym_id' loop_ _item_examples.case O 2B3 save_ save__ccp4_refine_tls_group.beg_label_seq_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ccp4_refine_tls_group.beg_label_seq_id' _item.category_id ccp4_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_ccp4_refine_tls_group.beg_label_seq_id' '_atom_site.label_seq_id' loop_ _item_examples.case 1 303 save_ save__ccp4_refine_tls_group.beg_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_ccp4_refine_tls_group.beg_auth_seq_id' _item.category_id ccp4_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_ccp4_refine_tls_group.beg_auth_seq_id' '_atom_site.auth_seq_id' loop_ _item_examples.case 1 5A save_ save__ccp4_refine_tls_group.end_label_asym_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ccp4_refine_tls_group.end_label_asym_id' _item.category_id ccp4_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_ccp4_refine_tls_group.end_label_asym_id' '_atom_site.label_asym_id' loop_ _item_examples.case O 2B3 save_ save__ccp4_refine_tls_group.end_label_seq_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ccp4_refine_tls_group.end_label_seq_id' _item.category_id ccp4_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_ccp4_refine_tls_group.end_label_seq_id' '_atom_site.label_seq_id' loop_ _item_examples.case 1 303 save_ save__ccp4_refine_tls_group.end_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_ccp4_refine_tls_group.end_auth_seq_id' _item.category_id ccp4_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_ccp4_refine_tls_group.end_auth_seq_id' '_atom_site.auth_seq_id' loop_ _item_examples.case 1 5A save_ save__ccp4_refine_tls_group.selection _item_description.description ; A description of the subset of atoms in the specified range included in the TLS fragment. ; _item.name '_ccp4_refine_tls_group.selection' _item.category_id ccp4_refine_tls_group _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail all ; all atoms in specified range ; mnc ; main chain atoms only ; sdc ; side chain atoms only ; save_ # save__refine.ccp4_solvent_vdw_probe_radii _item_description.description ; CCP4 solvent proble van der Waals radii ; _item.name '_refine.ccp4_solvent_vdw_probe_radii' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine.ccp4_solvent_ion_probe_radii _item_description.description ; CCP4 solvent ion proble radii ; _item.name '_refine.ccp4_solvent_ion_probe_radii' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine.ccp4_solvent_shrinkage_radii _item_description.description ; CCP4 solvent shrinkage radii ; _item.name '_refine.ccp4_solvent_shrinkage_radii' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ #----------------------------------------------------------- save__refln.ccp4_SAD_phase_anom _item_description.description ; The anomalous difference amplitude ; _item.name '_refln.ccp4_SAD_phase_anom' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_SAD_phase_anom_sigma' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln.ccp4_SAD_phase_anom_sigma _item_description.description ; The standard uncertainty (e.s.d.) of _refln.ccp4_SAD_phase_anom ; _item.name '_refln.ccp4_SAD_phase_anom_sigma' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_SAD_phase_anom' _item_related.function_code associated_value _item_type.code float _item_units.code arbitrary save_ save__refln.ccp4_SAD_F_meas_plus_au _item_description.description ; The measured value of the structure factor in arbitrary units for hkl. ; _item.name '_refln.ccp4_SAD_F_meas_plus_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_SAD_F_meas_plus_sigma_au' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln.ccp4_SAD_F_meas_plus_sigma_au _item_description.description ; The standard uncertainty (e.s.d.) of _refln.ccp4_SAD_F_meas_plus_au, in arbitrary units fo hkl. ; _item.name '_refln.ccp4_SAD_F_meas_plus_sigma_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_SAD_F_meas_plus_au' _item_related.function_code associated_value _item_type.code float _item_units.code arbitrary save_ save__refln.ccp4_SAD_F_meas_minus_au _item_description.description ; The measured value of the structure factor in arbitrary units for -h,-k,-l. ; _item.name '_refln.ccp4_SAD_F_meas_minus_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_SAD_F_meas_minus_sigma_au' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln.ccp4_SAD_F_meas_minus_sigma_au _item_description.description ; The standard uncertainty (e.s.d.) of _refln.ccp4_SAD_F_meas_minus_au, in arbitrary units for -h,-k,-l. ; _item.name '_refln.ccp4_SAD_F_meas_minus_sigma_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_SAD_F_meas_minus_au' _item_related.function_code associated_value _item_type.code float _item_units.code arbitrary save_ save__refln.ccp4_SAD_HL_A_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * cos(alphah~calc~) A~iso~ = ----------------------------------------------- E2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 21/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model alphah~calc~ = the calculated phase from the heavy atom model ; _item.name '_refln.ccp4_SAD_HL_A_iso' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.ccp4_SAD_HL_B_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * sin(alphah~calc~) B~iso~ = ----------------------------------------------- E2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 21/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model alphah~calc~ = the phase calculated from the heavy atom model ; _item.name '_refln.ccp4_SAD_HL_B_iso' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.ccp4_SAD_HL_C_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection for this derivative. -Fp~obs~^2^ * [sin(alphah~calc~)2^ - cos(alphah~calc~)2^] C~iso~ = ------------------------------------ E2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 21/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model alphah~calc~ = the phase calculated from the heavy atom model ; _item.name '_refln.ccp4_SAD_HL_C_iso' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.ccp4_SAD_HL_D_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection for this derivative. -2.0 * Fp~obs~^2^ * sin(alphah~calc~)2^ * cos(alphah~calc~)2^ D~iso~ = ---------------------------------------- E2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 21/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure factor amplitude of the native Fph~obs~ = the observed structure factor amplitude of the derivative Fh~calc~ = the calculated structure factor amplitude from the heavy atom model alphah~calc~ = the phase calculated from the heavy atom model ; _item.name '_refln.ccp4_SAD_HL_D_iso' _item.category_id refln _item.mandatory_code no _item_type.code float save_ #--------------------------------------------------------------------------- save__refln.ccp4_I_plus _item_description.description ; The measured value of the intensity in measured units for hkl. ; _item.name '_refln.ccp4_I_plus' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_I_plus_sigma' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln.ccp4_I_plus_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the intensity, in the measured units for hkl. ; _item.name '_refln.ccp4_I_plus_sigma' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_I_plus' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln.ccp4_I_minus _item_description.description ; The measured value of the intensity in measured units for -h,-k,-l. ; _item.name '_refln.ccp4_I_minus' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_I_minus_sigma' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln.ccp4_I_minus_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the intensity, in the measured units for -h,-k,-l. ; _item.name '_refln.ccp4_I_minus_sigma' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.ccp4_I_minus' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ ### EOF mmcif_ccp4-def-1.dic