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(82) BNF; magic string; extension to mmCIF
- To: COMCIFS@iucr
- Subject: (82) BNF; magic string; extension to mmCIF
Dear Colleagues
Thanks to everyone who responded directly to David Brown regarding the vote
on the revised terms of reference for COMCIFS. I'm sorry that it is taking
me so long to pick up all the threads and unfinished business from my
unexpected trip away during late February.
This time I have a couple of queries from Peter Murray-Rust (PMR>) and
a request for technical approval of a set of data items to extend the
mmCIF dictionary.
D82.1 BNF description of STAR/CIF/dictionary CIF format
-------------------------------------------------------
PMR> Is there a definitive statement in precise terms (e.g. in BNF) of (a)
PMR> CIF (b) 'dictionary-enhanced CIF' (i.e. CIF-with-save-frames)? Although
PMR> there is prose describing CIF there are places where it is not clear. For
PMR> people coming from outside the Crystallographic community there has to be
PMR> a precise definition of the language.
PMR>
PMR> If there *is* a BNF or equivalent, could it please be mounted on iucr.org?
The "Backus-Naur Form" is a formal description of the syntax of a computer
language. Nick Spadaccini and Peter Keller worked some time ago on a STAR
BNF, and I append the last version of their work below. Members are welcome
to review and criticise the proposal if they so desire. If there are no
objections, I would like to post this version on the CIF web page. I trust
that it (or a revised version) will also find its way into International
tables Vol. G. I invite a proposal for a CIF form, and also for the data
dictionary format (question from a computer science viewpoint - are one or
two different BNF specifications required for DDL1 and DDL2 dictionaries?
The DDL1 dictionaries conform fully to the CIF syntax; DDL2 dictionaries
also permit save frames).
==============================================================================
(Extracts from correspondence Date: Tue, 21 Nov 1995 12:10:17
From: Peter Keller <bsspak@bath.ac.uk>
To: Brian McMahon <bm@iucr.ac.uk>, Nick Spadaccini <nick@sdsc.edu>,
Sydney Hall <syd@crystal.uwa.edu.au>)
A third attempt at a specification for STAR
Why do CIF programmers need to know about STAR? I'm not a great expert on
database theory, but I don't think that anyone would contradict me in
saying that there are three broad aspects to using any datafile
format. They are:
1) Lexical considerations: what arrangements of bytes (characters) are
allowed, how they are grouped into tokens (words), and how those tokens are
classified into various types.
2) Syntax or grammar: the function which each type of token has, the order
in which tokens can follow each other, and how they are grouped into larger
structures.
3) Semantics: the interpretation of the data, what it means, manipulation
of the information which it expresses.
For example, a sequence of non-space characters which begins with an
underscore is a token of type 'data name' [lexical analysis]. It identifies
a data value (which is another type of token), and must either be followed
by a single data value, or appear in the header of a loop structure
[syntactical analysis]. The semantics involve recognising the data name
itself, in order to attach a meaning to the data value which it identifies.
Now, for CIF's, STAR specifies all of the lexical and syntactical aspects,
as well as a very few of the semantics. (The bulk of the semantical aspects
of CIF are dealt with by DDL's and dictionaries). This means that any CIF
file must be a valid STAR file, which means, in turn, that CIF programmers
must be aware of the whole of the STAR syntax, not just the parts which are
used by CIF. For example, in STAR, a framecode is a sequence of non-blank
characters, the first of which is a '$'. Even though framecodes are not
used in CIF's, it is still necessary to be aware of them, to avoid trying
to start a non quoted text string with a '$'.
The most recent published specification of the STAR syntax appears in "The
STAR File: Detailed Specifications" (S.R.Hall and N.Spadaccini, J. Chem.
Inf. Comput. Sci, 34, p505-508 (1994) ). This paper was itself intended to
improve the precision of an earlier specification; however, code based on
the newer specification still cannot be relied on to parse STAR files
accurately without making certain assumptions during lexical analysis.
Also, there were a number of typographical errors and omissions.
Hopefully, this specification will be useful to programmers writing their
own lexers and parsers directly. It is also intended to be easily
convertible to a working parser using code generators such as yacc/lex,
bison/flex, PCCTS, PRECCX, etc., with a minimum of interpretation required
from the programmer. It seeks to consolidate existing practice, and to
prevent ambiguities arising in the future. It is not intended to extend the
syntax.
N.B. This syntax should be read in conjunction with the JCICS paper.
A few notes on the table:
1). A standard set of symbols is used in this table. They are:
* means "zero or more"
+ means "at least one"
{....} groups a number of terms together.
[....] means "optional" (in a syntactic sense only - it does not mean
that inserting or removing the item has no
effect on the data representation being expressed.)
| means "or"
::= means "is defined to be"
<...> is a syntactic or lexical construction. If it appears on the
right hand side of a definition, the definition of that term is subtituted in.
2). Items whose names are in UPPER CASE on the left-hand side of the
definitions below, are those which would conventionally be considered as
tokens during lexical analysis. This is only intended as a guide - in
particular, tokens which can be of arbitrary length, may need to be
processed in smaller portions in a particular implementation. For CIF's,
this is only a consideration for the <semi_colon_bounded_text_string> type
- all others are limited in size by the 80 characters to a line rule.
3). Comments. There are two possible ways of treating comments. The
characters from the initial '#' to the last character on the line
(inclusive) can simply be thrown away during lexical analysis. In this
case, all the <comment>* constructions can be dropped from the definition
below. (This is the treatment implied by the 1994 JCICS paper.)
However, an application may carry out an operation on the information
contained within a CIF (as opposed to the data structures themselves),
generating a new CIF in the process. In such a case, it will normally be
useful to retain comments in their original places in the output file, as
far as possible. For this purpose, the comment specifications below can be
used. The approach taken is that a comment is defined to be a token
type. The file can start with an arbitrary number of comments, and each
non-comment token can be followed by an arbitrary number of comments.
4). Whitespace. This is a potential minefield for precise definition,
since which whitespace characters are allowed at particular places in a
STAR file (or indeed any text file or stream) is system and protocol
dependent. Getting to grips with the implications of the BNF table is
hard work, so the rules are summarised here.
Basically, six whitespace characters are permitted, all of which
may separate tokens (in the sense of note 2 above, and the upper case
definitions in the table below):
ht (ASCII 9)
lf (ASCII 10)
vt (ASCII 11)
ff (ASCII 12)
cr (ASCII 13)
' ' (ASCII 32)
Of these, vt and ff may only appear between tokens, not within them. ht and
' ' (i.e. <blank>) are allowed within quoted strings, comments and
semi-colon bounded strings. The latter will contain <newline>'s as well.
ff (but not vt) is taken to imply a new line, and so can introduce a
semi-colon bounded text string and terminate a comment (and also delimit
lines for the purposes of lines in a CIF being no more than 80
characters).
<newline> subsumes cr and lf, but this does not imply that either or both
are appropriate in any particular context. Some specific possibilities are:
Unix <newline> :== <lf>
MacOS <newline> :== <cr>
MS-DOS <newline> :== <cr><lf> (raw file/fopen etc. in binary mode)
MS-DOS <newline> :== '\n' (fopen etc. in text mode)
* ASCII FTP <newline> :== <cr><lf> (RFC959)
* Gopher <newline> :== <cr><lf> (RFC1436)
* HTTP <newline> :== [<cr>]<lf> (strictly <cr><lf>, but the
recommendation for tolerant http clients and servers states that: "Lines
should be regarded as terminated by the Line Feed, and the preceeding
Carriage Return character ignored."
(http://www.w3.org/pub/WWW/Protocols/HTTP1.0/draft-ietf-http-v10-spec-04.txt
section 2.2 and Appendix B).
* For ftp, gopher and http, think of a network client parsing a STAR
information stream directly from a server's port.
Other environments may require extension of this picture - as a programmer,
you have to be familiar with your own development enviromnent.
Note that tokens must be separated by at least one whitespace character.
In particular, it means that constructions such as the following are not
allowed, even though they are, in principle, interpretable:
_data.item_1
; a bit of
multi-line
text
;_data.item_2 .....
There must be at least one whitespace character after the second semi-colon
here.
5). Quoted text strings. These are defined so that a quote of the same
type as that which encloses a string, can also appear in the middle of
that string, as long as it is followed by a non-blank character. For
example, in:
_data.item 'Peter's example'
the middle quote does not close the text string, because it is not followed
by the whitespace character which is necessary to separate tokens. It is
the third quote which fulfills that function.
Note, though, that the DDL version 2.x, and mmCIF, restrict the characters
which may appear in data items (check the contents of the ITEM_TYPE_LIST
category in the dictionary). The above example only became legal in a
macromolecular CIF at version 0.7.28 of mmCIF (1995-10-6), and then only
for certain types of data.
6). Non-quoted text string. This complicated-looking construction is
intended to distinguish between a semi-colon appearing in column 1, or
elsewhere on the line:
;A_few_characters
would be the first line of a <semi_colon_bounded_text_string>, and
;A_few_characters
is a <non_quoted_text_string> .
Also, a <non_quoted_text_string> is now explicitly prevented from starting
with a quote, so it is illegal at the lexical level for an opening quote to
appear without a corresponding closing quote on the same line.
7). During lexical analysis, tokens which begin with a fixed sequence of
more than one character must be checked for first. (These are
<global_heading>, <data_heading>, <save_heading>, and the fixed tokens
"loop_", "save_" and "stop_" ). Other token types can now be determined
just from the whitespace character preceding the token (the 'leading
context') and the first character of the token itself.
Note that of these tokens, only <data_heading> and "loop_" can appear in a
CIF. (CIF dictionaries are not themselves CIF data files, so they may
contain any of these tokens.) However, this does not mean that it is
unnecessary for a CIF application to check for the other tokens, since they
still have meaning at the STAR level. If you want to assign the sequence of
characters (s, t, o, p, _) to a data name in a CIF, you have to quote it:
_data.item 'stop_'
otherwise the CIF will not be a legal STAR file (or, at the very least,
will not mean what you want it to mean).
8). Loops. It is a requirement of STAR that a loop structure must have
complete loop packets, i.e. the number of data values in a nested loop
which are assigned to a particular <data_loop_definition> at its
particular level of nesting, must be an integral multiple of the number of
<data_name>'s in that <data_loop_definition>.
CIF's don't allow nested loops, so this condition can be expressed in a
simpler way: the number of data values in a loop structure must be an
integral multiple of the number of data names in the loop header. This
sounds obvious, but it is very difficult to express in a table such as the
one below, so it is re-stated here.
<star_file> ::= <comment>* {<data_block> | <global_block>}*
<data_block> ::= <data_heading> <comment>* <data_block_body>*
<global_block> ::= <global_heading> <comment>* <data_block_body>+
<GLOBAL_HEADING> ::= global_
<data_block_body> ::= {<data> | <save_frame>}+
<data> ::= <data_name> <comment>* <data_value> <comment>*
| <data_loop>
<save_frame> ::= <save_heading> <comment>* <data>* save_ <comment>*
<data_loop> ::= loop_ <comment>* <data_loop_definition>
<data_loop_values>
<data_loop_defintion> ::= <data_loop_field>+
<data_loop_field> ::= { <data_name> | <nested_loop> } <comment>*
<nested_loop> ::= loop_ <comment>* <data_loop_definition> [stop_]
<data_loop_values> ::= <data_loop_item>+
<data_loop_item> ::= { <data_value> | stop_ } <comment>*
<data_value> ::= <non_quoted_text_string>
| <double_quoted_text_string>
| <single_quoted_text_string>
| <semi_colon_bounded_text_string>
| <frame_code>
<DATA_HEADING> ::= data_ <non_blank_char>+
<DATA_NAME> ::= _ <non_blank_char>+
<SAVE_HEADING> ::= save_ <non_blank_char>+
<NON_QUOTED_TEXT_STRING> ::= { { <line_begin><ordinary_char> }
| {<line_space> {<ordinary_char>|<semi_colon>} } }
<non_blank_char>*
<DOUBLE_QUOTED_TEXT_STRING> ::= <D_quote> <D_quote_string> <D_quote>
<D_quote_string> ::= {<D_quote> <non_blank_char> |
<not_a_D_quote>}*
<SINGLE_QUOTED_TEXT_STRING> ::= <S_quote> <S_quote_string> <S_quote>
<S_quote_string> ::= {<S_quote> <non_blank_char> |
<not_a_S_quote>}*
<SEMI_COLON_BOUNDED_TEXT_STRING>
::= <line_begin><semi_colon> <char>* <newline>
<line_of_text>*
<semi_colon>
<FRAME_CODE> ::= $<non_blank_char>+
<COMMENT> ::= { <line_space> | <line_begin> } #<char>* <line_begin>
<line_begin> ::= beginning of a new line of input (i.e. leading
{ <newline> | <form_feed> } )
<blank> ::= space (ASCII 32)
| horizontal tab (ASCII 9)
<line_space> ::= end of leading, or start of trailing
{<blank> | <vert_tab>}
<non_blank_char> ::= ! shriek -> ~ tilde (ASCII 33-126)
<char> ::= <blank>
| <non_blank_char>
<line_of_text> ::= [ <not_a_semi_colon><char>* ] <newline>
<newline> ::= End of line character(s) as defined by
operating system, file structure and system
libraries.
<form_feed> ::= ff (ASCII 12)
<vert_tab> ::= vt (ASCII 11)
<D_quote> ::= " (ASCII 34)
<S_quote> ::= ' (ASCII 39)
<not_a_D_quote> ::= ! shriek (ASCII 33)
| # sharp -> ~ tilde (ASCII 35-126)
| <blank>
<not_a_S_quote> ::= ! shriek -> & ampersand (ASCII 33-38)
| ( left bracket -> ~ tilde (ASCII 40-126)
| <blank>
<ordinary_char> ::= ! shriek (ASCII 33)
| % percent (ASCII 37)
| & ampersand (ASCII 38)
| ( left bracket -> : colon (ASCII 40-58)
| < less than -> ^ caret (ASCII 60-94)
| ` backquote -> ~ tilde (ASCII 96-126)
<not_a_semi_colon> ::= ! shriek -> : colon (ASCII 33-58)
| < less than -> ~ tilde (ASCII 60-126)
| <blank>
<semi_colon> ::= ; semicolon (ASCII 59)
==============================================================================
D89.2 "Magic number" to identify CIF format internally
------------------------------------------------------
PMR> Since dictionaries and data instances have different syntax it is
PMR> important that the files have some internal means of identifying their
PMR> type. [More generally perhaps CIF files should have a magic string at the
PMR> top to indicate what their type is? e.g.
PMR> #CIF DDL1.0 Crystallographic Information File (iucr.org)]
PMR>
PMR> Data will be increasingly be delivered by servers as streams (i.e. without
PMR> suffixes, although hopefully with chemical/MIME stamps :-). For example,
PMR> what does:
PMR> http://www.pdb.bnl.gov/pdb-cgi/send-cif?foo
PMR> send - a dictionary or an instance? The author of client-side software
PMR> will need to know what is apparently sent so they can check on integrity.
Note the decision by the imgCIF/CBF community to use the magic string
###_CRYSTALLOGRAPHIC_BINARY_FILE: VERSION 1.0
at the start of a crystallographic binary file.
D89.3 Request for technical approval of extension to mmCIF dictionary
---------------------------------------------------------------------
The following request has been submitted by the mmCIF dictionary management
group. Note their proposal to release these data items to the community for
content review on April 15. Absence of comment by a COMCIFS member by April
15 will be taken as approval of the technical compliance of the submitted
items with the CIF standard.
> To COMCIFS -
>
> In accordance with the time-table established by the executive of the mmCIF
> working group, we are now ready to submit to COMCIFS the data items that
> will constitute the extension of the mmCIF dictionary from Version 1.0 to
> Version 2.0.
>
> These proposed new data itmes were submitted from the community (in this
> case, from Kim Henrick of EBI), reviewed by the appropriate member(s) of
> the panel of editors of the mmCIF dictionary for content, and then given
> further editorial review by the executive of the mmCIF working group. It
> is our understanding that the next step in the process is to submit the
> data items to COMCIFS for a quick review of technical compliance with the
> CIF standard, before submitting them for review by the crystallographic
> community. Following community review and revision, we will submit these
> data items to COMCIFS for formal approval.
>
> We would like to release them for community review by April 15, and hope
> than the members of COMCIFS will find them technically sound in short
> order so that the process of community review may begin.
>
> Paula Fitzgerald
> Helen Berman
> John Westbrook
The data items are appended to this circular. I confirm that the file
fragment exhibits no syntax errors under 'vcif'.
Regards
Brian
_______________________________________________________________________________
Brian McMahon tel: +44 1244 342878
Research and Development Officer fax: +44 1244 314888
International Union of Crystallography e-mail: bm@iucr.ac.uk
5 Abbey Square, Chester CH1 2HU, England bm@iucr.org
_______________________________________________________________________________
- - - - -
#################
## PHASING_MIR ##
#################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save__phasing_MIR.d_res_high
_item_description.description
; The highest resolution for the interplanar spacing in the
reflection data used for the native data set. This is the
smallest d value.
;
_item.name '_phasing_MIR.d_res_high'
_item.category_id phasing_MIR
_item.mandatory_code yes
_item_aliases.alias_name '_phasing_MIR.ebi_d_res_high'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR.d_res_low
_item_description.description
; The lowest resolution for the interplanar spacing in the
reflection data used for the native data set. This is the
largest d value.
;
_item.name '_phasing_MIR.d_res_low'
_item.category_id phasing_MIR
_item.mandatory_code yes
_item_aliases.alias_name '_phasing_MIR.ebi_d_res_low'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR.fom
_item_description.description
; The mean value of the figure of merit m for all reflections
phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.fom'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.fom_acentric
_item_description.description
; The mean value of the figure of merit m for the acentric
reflections phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.fom_acentric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.fom_centric
_item_description.description
; The mean value of the figure of merit m for the centric
reflections phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.fom_centric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.reflns
_item_description.description
; The total number of reflections phased in the native data set.
;
_item.name '_phasing_MIR.reflns'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_acentric
_item_description.description
; The number of acentric reflections phased in the native data
set.
;
_item.name '_phasing_MIR.reflns_acentric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_centric
_item_description.description
; The number of centric reflections phased in the native data
set.
;
_item.name '_phasing_MIR.reflns_centric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_criterion
_item_description.description
; Criterion used to limit the reflections used in the phasing
calculations.
;
_item.name '_phasing_MIR.reflns_criterion'
_item.category_id phasing_MIR
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_criteria'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item.mandatory_code no
_item_type.code text
_item_examples.case '> 4 \s(I)'
save_
#####################
## PHASING_MIR_DER ##
#####################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save__phasing_MIR_der.power_acentric
_item_description.description
; The mean phasing power P for acentric reflections in this
derivative.
Phasing power is <FH / Lack_of_closure>.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure factor amplitude of this
derivative
Fph~calc~ = the calculated structure factor amplitude of this
derivative
Fh~calc~ = the calculated structure factor amplitude from the
heavy atom model
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_der.power_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_power_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.power_centric
_item_description.description
; The mean phasing power P for centric reflections in this
derivative.
Phasing power is <FH / Lack_of_closure>.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure factor amplitude of the
derivative
Fph~calc~ = the calculated structure factor amplitude of the
derivative
Fh~calc~ = the calculated structure factor amplitude from the
heavy atom model
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_der.power_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_power_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_acentric
_item_description.description
; Residual factor R~cullis~ for acentric reflections in this
derivative.
Cullis R factor is <Lack_of_closure>/<Isomorphous difference>.
NB: This is tabulated for acentric and anomalous terms,
extending the former definition.
;
_item.name '_phasing_MIR_der.R_cullis_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_anomalous
_item_description.description
; Residual factor R~cullis~ for anomalous reflections in this
derivative.
Cullis R factor is <Lack_of_closure>/<Isomorphous difference>.
NB: This is tabulated for acentric and anomalous terms,
extending the former definition.
Anomalous difference is |FPHi(+) - FPHi(-)|.
Calculated anomalous difference is 2 * FHi" * sin(PHIx)
where PHIx is the protein phase.
Lack of closure is | Anom.Diff - Calc.Anom.Diff|
Cullis Rfactor is <Lack_of_closure>/ <Anomalous difference>
This is tabulated for acentric terms. Any value <1.0 means
there is some contribution to the phasing from the
anomalous data.
Sum(h) Sum(phi) prob(phi) |Dano_obs(h) - Dano_calc(h,phi)|
RC(ano) = ----------------------------------------------------------
Sum(h) |Dano_obs(h)|
;
_item.name '_phasing_MIR_der.R_cullis_anomalous'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_anomalous'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_centric
_item_description.description
; Residual factor R~cullis~ for centric reflections in this
derivative.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
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
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.
;
_item.name '_phasing_MIR_der.R_cullis_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.reflns_acentric
_item_description.description
; The number of acentric reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_der.reflns_anomalous
_item_description.description
; The number of anomalous reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_anomalous'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_anomalous'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_der.reflns_centric
_item_description.description
; The number of centric reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
##########################
## PHASING_MIR_DER_SITE ##
##########################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save__phasing_MIR_der_site.occupancy_anom
_item_description.description
; The relative anomalous occupancy of the atom type
present at this heavy-atom site in a given derivative.
This atom occupancy will probably be on an arbitrary scale.
;
_item.name '_phasing_MIR_der_site.occupancy_anom'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_anom_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.occupancy_anom_esd
_item_description.description
; The standard uncertainty (e.s.d) of
_phasing_MIR_der_site.occupancy_anom.
;
_item.name '_phasing_MIR_der_site.occupancy_anom_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom_esd'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_default.value 0.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_anom'
_item_related.function_code associated_value
_item_type.code float
save_
save__phasing_MIR_der_site.occupancy_iso
_item_description.description
; The relative real isotropic occupancy of the atom type
present at this heavy-atom site in a given derivative.
This atom occupancy will probably be on an arbitrary scale.
;
_item.name '_phasing_MIR_der_site.occupancy_iso'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_iso_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.occupancy_iso_esd
_item_description.description
; The standard uncertainty (e.s.d.) of
_phasing_MIR_der_site.occupancy_iso.
;
_item.name '_phasing_MIR_der_site.occupancy_iso_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso_esd'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_default.value 0.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_iso'
_item_related.function_code associated_value
_item_type.code float
save_
#######################
## PHASING_MIR_SHELL ##
#######################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save__phasing_MIR_shell.fom_acentric
_item_description.description
; The mean value of the figure of merit m for acentric reflections
in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR_shell.fom_acentric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.fom_centric
_item_description.description
; The mean value of the figure of merit m for centric reflections
in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR_shell.fom_centric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.reflns_acentric
_item_description.description
; The number of acentric reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns_acentric'
_item.category_id phasing_mir_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_shell.reflns_centric
_item_description.description
; The number of centric reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns_centric'
_item.category_id phasing_mir_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
###################
## REFLN_SYS_ABS ##
###################
#
###########################
## proposed new category ##
###########################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save_REFLN_SYS_ABS
_category.description
; Data items in the REFLN_SYS_ABS category record details about
the reflection data that should be systematically absent,
given the designated space group.
;
_category.id refln_sys_abs
_category.mandatory_code no
loop_
_category_key.name '_refln_sys_abs.index_h'
'_refln_sys_abs.index_k'
'_refln_sys_abs.index_l'
loop_
_category_group.id 'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - completely arbitrary
;
;
loop_
_refln_sys_abs.index_h
_refln_sys_abs.index_k
_refln_sys_abs.index_l
_refln_sys_abs.I
_refln_sys_abs.sigmaI
_refln_sys_abs.I_over_sigmaI
0 3 0 28.32 22.95 1.23
0 5 0 14.11 16.38 0.86
0 7 0 114.81 20.22 5.67
0 9 0 32.99 24.51 1.35
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refln_sys_abs.I
_item_description.description
; The measured value of the intensity in arbitrary units.
;
_item.name '_refln_sys_abs.I'
_item.category_id refln_sys_abs
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refln_sys_abs.I'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_related.related_name
_item_related.function_code '_refln_sys_abs.sigmaI'
associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code arbitrary
save_
save__refln_sys_abs.I_over_sigmaI
_item_description.description
; The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used
to evaluate whether a reflection that should be systematically
absent according to the designated space group is in fact
absent.
;
_item.name '_refln_sys_abs.I_over_sigmaI'
_item.category_id refln_sys_abs
_item_aliases.alias_name '_ebi_refln_sys_abs.I_over_sigma'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item.mandatory_code no
_item_type.code float
save_
save__refln_sys_abs.index_h
_item_description.description
; Miller index h of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to
the cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_h'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.h'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_k'
'_refln_sys_abs.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.index_k
_item_description.description
; Miller index k of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to the
cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_k'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.k'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_h'
'_refln_sys_abs.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.index_l
_item_description.description
; Miller index h of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to the
cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_l'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.l'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_h'
'_refln_sys_abs.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.sigmaI
_item_description.description
; The standard uncertainty (e.s.d.) of _refln_sys_abs.I, in
arbitrary units.
;
_item.name '_refln_sys_abs.sigmaI'
_item.category_id refln_sys_abs
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refln_sys_abs.sigmaI'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_related.related_name
_item_related.function_code '_ebi_refln_sys_abs.I'
associated_value
_item_type.code float
_item_units.code arbitrary
save_
############
## REFINE ##
############
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
###################################################
## Submitted by Kim Henrick ##
## Content review by Dale Tronrud - Mar 19, 1988 ##
## Editorial review by HB, JW and PMDF ##
###################################################
save__refine.correlation_coeff_Fo_to_Fc
_item_description.description
; The correlation coefficient between Fobs and Fcalcs for
reflection included in refinement
Correlation coefficients is scale independent and gives
an idea of quality of refined model
sum~i~(Fo~i~ Fc~i~ -<Fo> <Fc>)
R_corr = ------------------------------------------------
SQRT{sum~i~(Fo~i~)^2-<Fo>^2} SQRT{sum~i~(Fc~i~)^2-<Fc>^2}
Fo = observed structure factors
Fc = calculated structure factors
<> = denotes average value of data
Summation is over reflections included in refinement
;
_item.name '_refine.correlation_coeff_Fo_to_Fc'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.correlation_coeff_Fo_to_Fc_free
_item_description.description
; The correlation coefficient between Fobs and Fcalcs not
included in refinement (free reflections)
Correlation coefficients is scale independent and gives an
idea of quality of refined model
sum~i~(Fo~i~ Fc~i~ -<Fo> <Fc>)
R_corr = ------------------------------------------------
SQRT{sum~i~(Fo~i~)^2-<Fo>^2} SQRT{sum~i~(Fc~i~)^2-<Fc>^2}
Fo = observed structure factors
Fc = calculated structure factors
<> = denotes average value of data
Summation is over reflections not included
(free reflections) in refinement
;
_item.name '_refine.correlation_coeff_Fo_to_Fc_free'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc_free'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_ESU_B
_item_description.description
; Overall estimated standard uncertainties of thermal parameters
based on Maximum likelihood residual.
Overall ESU gives an idea about uncertainties of B-values of
averagely defined atoms (atoms with B-values equal to average
B-value)
N_a
(sigma_B)^2 = 8 ----------------------------------------------
sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^4}
SUM_AS = (sigma_A)^2/Sigma^2)
N_a = number of atoms
Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = is form factor of atoms
delta_x = expected error
m = is figure of merit of phases of reflection
included in summation delta_x expected error
s = reciprocal space vector
epsilon = multiplicity of diffracting plane
summation is over all reflections included in refinement
Reference for sigma_A estimation:
"Refinement of Macromolecular Structures by the
Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and
E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255
Reference for ESU_ML estimation:
"Simplified error estimation a la Cruickshank in macromolecular
crystallography", Murshudov G.N. & Dodson E.J. in the "CCP4
Newsletter on protein crystallography" Number 33 ed. M.Winn
;
_item.name '_refine.overall_ESU_B'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_B'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_ESU_ML
_item_description.description
; Overall estimated standard uncertainties of positional
parameters based on Maximum likelihood residual.
Overall ESU gives an idea about uncertainties in the position
of averagely defined atoms (atoms with B-values equal to
average B-value)
3 N_a
(sigma_X)^2 = -----------------------------------------------------
8 pi^2 sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^2}
SUM_AS = (sigma_A)^2/Sigma^2)
N_a = number of atoms
Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = is formfactor of atoms
delta_x = expected error
m = is figure of merit of phases of reflection
included in summation delta_x expected error
s = reciprocal space vector
epsilon = multiplicity of diffracting plane
summation is over all reflections included in refinement
Reference for sigma_A estimation:
"Refinement of Macromolecular Structures by the
Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and
E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255
Reference for ESU_ML estimation:
Simplified error estimation a la Cruickshank in macromolecular
crystallograpy Murshudov G.N. & Dodson E.J. in the "CCP4
Newsletter on protein crystallography" Number 33 ed. M.Winn
;
_item.name '_refine.overall_ESU_ML'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_ML'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_ESU_R_Cruickshanks_DPI
_item_description.description
; Overall estimated standard uncertainties of thermal parameters
based on crystallographic R-value
Overall ESU gives an idea about uncertainties of B-values of
averagely defined atoms (atoms with B-values equal to average
B-value)
N_a
(sigma_B)^2 = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3)
(N_o-N_p)
N_a = number of atoms
N_o = number of reflections included in refinement
N_p = number of refined parameters
R_value = conventional crystallographic R-value
D_min = maximum resolution
C = completeness of data
Reference for ESU_ML estimation:
Cruickshank, in the "Refinement of macromolecular structures"
CCP4 study weekend
Simplified error estimation a la Cruickshank in
macromolecular crystallography, Murshudov G.N. & Dodson E.J.
in the "CCP4 Newsletter on protein crystallography" Number 33
ed. M.Winn
;
_item.name '_refine.overall_ESU_R_Cruickshanks_DPI'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_R_Cruickshanks_DPI'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_ESU_Rfree
_item_description.description
; Overall estimated standard uncertainties of thermal parameters
based on free R-value
Overall ESU gives an idea about uncertainties of B-values of
averagely defined atoms (atoms with B-values equal to average
B-value)
N_a
(sigma_B)^2 = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3)
N_o
N_a = number of atoms
N_o = number of reflections included in refinement
N_p = number of refined parameters
R_free = conventional free crystallographic R-value calculated
using reflections not included in refinement
D_min = maximum resolution
C = completeness of data
Reference for ESU_ML estimation:
Cruickshank, in the "Refinement of macromolecular structures"
CCP4 study weekend
Simplified error estimation a la Cruickshank in macromolecular
crystallography, Murshudov G.N. & Dodson E.J.
in the "CCP4 Newsletter on protein crystallography" Number 33
ed. M.Winn
;
_item.name '_refine.overall_ESU_Rfree'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_Rfree'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_FOM_free_Rset
_item_description.description
; Average figure of merit of phases of reflections not included
in refinement
This value is derived from likelihood function.
fom = I_1(X)/I_0(X)
I_0, I_1 = zero and first ordered modified Bessel function
first kind X = sigma_A |E_o| |E_c|/SIGMA
E_o, E_c = normalized observed and calculated structure
factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = formfactor of atoms
delta_x = expected error
SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
sigma_{E;exp} = uncertainties of normalized observed structure
factors
epsilon = multiplicity of diffracting plane
Reference for sigma_A estimation:
"Refinement of Macromolecular Structures by the
Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and
E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255
;
_item.name '_refine.overall_FOM_work_Rset'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_FOM_work_Rset'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_FOM_work_Rset
_item_description.description
; Average figure of merit of phases of reflections included in
refinement.
This value is derived from likelihood function.
fom = I_1(X)/I_0(X)
I_0, I_1 = zero and first ordered modified
Bessel function first kind
X = sigma_A |E_o| |E_c|/SIGMA
E_o, E_c = normalized observed and calculated structure
factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = is formfactor of atoms
delta_x = expected error
SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
sigma_{E;exp} = uncertainties of normalized observed
structure factors
epsilon = multiplicity of diffracting plane
Reference for sigma_A estimation:
"Refinement of Macromolecular Structures by the
Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and
E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255
;
_item.name '_refine.overall_FOM_work_Rset'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_FOM_work_Rset'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
####################
## REFINE_ANALYZE ##
####################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
###################################################
## Submitted by Kim Henrick ##
## Content review by Dale Tronrud - Jan 13, 1998 ##
## Editorial review by HB, JW and PMDF ##
###################################################
save__refine_analyze.RG_d_res_high
_item_description.description
; The value of the high resolution cutoff, in Angstrom,
used in calculation of the Hamilton generalized
R factor (RG) stored in refine_analyze.RG_work and
_refine_analyze.ls_RG_free.
;
_item.name '_refine_analyze.RG_d_res_high'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_high'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.RG_d_res_low
_item_description.description
; The value of the low resolution cutoff, in Angstrom,
used in calculation of the Hamilton generalized
R factor (RG) stored in refine_analyze.ls_RG_work and
_refine_analyze.ls_RG_free.
;
_item.name '_refine_analyze.RG_d_res_low'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_low'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.RG_free
_item_description.description
; The Hamilton generalized R-factor (see W.C. Hamilton (1965)
Acta Cryst., 18, 502-510. ) for all reflections that satisfy
the resolution limits established by
_refine_analyze.RG_d_res_high and
_refine_analyze.RG_d_res_low for the Free R set of
reflections that were excluded from the refinement.
/ sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)\
Rg = Sqrt| ----------------------------------------------------------------- |
\ sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j /
where
|Fobs| = the observed structure factor amplitudes
|Fcalc| = the calculated structure factor amplitudes
G = the scale factor which puts |Fcalc| on the
same scale as |Fobs|
w_{i,j} = the weight for the combination of the reflections
i and j.
sum_i and sum_j is taken over the specified reflections
When the covariance of the amplitude of reflection i and
reflection j is zero (i.e. the reflections are independent)
w{i,i} can be redefined as w_i and the nested sums collapsed
into one.
/ sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 \
Rg = Sqrt| ----------------------------------- |
\ sum_i w_i |Fobs|_i^2 /
;
_item.name '_refine_analyze.RG_free'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_free'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_analyze.RG_work
_item_description.description
; The Hamilton generalized R factor (see W.C. Hamilton
(1965) Acta Cryst., 18, 502-510. ) for all reflections
that satisfy the resolution limits established by
_refine_analyze.RG_d_res_high and
_refine_analyze.RG_d_res_low and for those
reflections included in the working set when a Free R set
of reflections are omitted from the refinement.
/ sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)\
Rg = Sqrt| ----------------------------------------------------------------- |
\ sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j /
where
|Fobs| = the observed structure factor amplitudes
|Fcalc| = the calculated structure factor amplitudes
G = the scale factor which puts |Fcalc| on the
same scale as |Fobs|
w_{i,j} = the weight for the combination of the reflections
i and j.
sum_i and sum_j is taken over the specified reflections
When the covariance of the amplitude of reflection i and
reflection j is zero (i.e. the reflections are independent)
w{i,i} can be redefined as w_i and the nested sums collapsed
into one.
/ sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 \
Rg = Sqrt| ----------------------------------- |
\ sum_i w_i |Fobs|_i^2 /
;
_item.name '_refine_analyze.RG_work'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_work'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_analyze.RG_work_free_ratio
_item_description.description
;
The observed RGfree/RGwork ratio. The expected RG ratio is
the value that should be achievable at the end of a structure
refinement when only random uncorrelated errors exist in data
and model provided that the observations are properly weighted.
When compared to the observed RG ratio it may indicate that a
structure has not reached convergence or a model has been over
refined with no corresponding improvement in the model.
See: I.J. Tickle, R.A. Laskowski and D.S. Moss, (1998)
"Rfree and the Rfree ratio: deviation of expected values of
cross-validation residuals used in macromolecular least-squares
refinement" Acta Cryst. D, in press
In an unrestrained refinement the ratio of RGfree/RGwork with
only random uncorrelated errors at convergence would only
depend on the number of reflections and the number of
parameters as:
sqrt[(f + m) / (f - m) ]
where f = number of included structure amplitudes and
target distances, and
m = number of parameters being refined.
In the restrained case, RGfree is calculated from a random
selection of residuals including both structure amplitudes
and restraints. When restraints are included in refinement
the RG ratio requires a term for the contribution to the
minimized residual at convergence, Drest, due to those
restraints:
Drest = r - sum (w_i . (a_i)^t . (H)^-1 a_i
Where
r is the number of geometrical, temperature factor and
other restraints
H is the (m,m) normal matrix given by A^t.W.A
W is the (n,n) symmetric weight matrix of the included
observations
A is the least-squares design matrix of derivatives of \
order (n,m)
a_i is the ith row of A
Then the expected RGratio becomes
sqrt [ (f + (m - r + Drest))/ (f - (m - r + Drest)) ]
The expected RGfree/RGwork is not yet included in the mmCIF
dictionary.
;
_item.name '_refine_analyze.RG_work_free_ratio'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_work_free_ratio'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
###############################
## REFINE_FUNCT_MINIMIZED ##
###############################
#
###########################
## proposed new category ##
###########################
#
###################################################
## Submitted by Kim Henrick ##
## Content review by Dale Tronrud - Jan 13, 1998 ##
## Editorial review by HB, JW and PMDF ##
###################################################
save_REFINE_FUNCT_MINIMIZED
_category.description
; Data items in the REFINE_FUNCT_MINIMIZED category record
details about the individual terms of the function minimized
during refinement.
;
_category.id refine_funct_minimized
_category.mandatory_code no
_category_key.name '_refine_funct_minimized.type'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on RESTRAIN refinement for the CCP4 text data set
toxd.
;
;
loop_
_refine_funct_minimized.type
_refine_funct_minimized.numTerms
_refine_funct_minimized.residual
'sum(W*Delta(Amplitude)^2' 3009 1621.3
'sum(W*Delta(Plane+Rigid)^2' 85 56.68
'sum(W*Delta(Distance)^2' 1219 163.59
'sum(W*Delta(U-tempfactors)^2' 1192 69.338
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_funct_minimized.numterms
_item_description.description
; The number observations in this term. For example, if the
term is residual of the X-ray data this item would contain
the number of reflections used in refinement.
;
_item.name '_refine_funct_minimized.numterms'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.NumTerms'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_funct_minimized.residual
_item_description.description
; The residual for this term of function which was minimized
in refinement.
;
_item.name '_refine_funct_minimized.residual'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.Residual'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_funct_minimized.type
_item_description.description
; The type of the function being minimized.
;
_item.name '_refine_funct_minimized.type'
_item.category_id refine_funct_minimized
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refine_funct_minimized.type'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code line
save_
save__refine_funct_minimized.weight
_item_description.description
; The weight applied to this term of the function which was
minimized in refinement.
;
_item.name '_refine_funct_minimized.weight'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.weight'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
#####################
## REFINE_LS_RESTR ##
#####################
#
###################################################
## proposed elaboration of an existing data item ##
###################################################
#
####################################################
## Submitted by Kim Henrick ##
## Content review by John Westbrook ##
## Kim Henrick approval of changes - Jan 22, 1998 ##
## Editorial review by HB, JW and PMDF ##
####################################################
save__refine_ls_restr.type
_item_description.description
; The type of the parameter being restrained.
An explicit set of data values are provided for programs Protin/
Prolsq (beginning with p_) and X-plor (beginning with x_).
As computer programs will evolve, these data values are given
as examples, and not as an enumeration list. Computer programs
converting a data block to a refinement table will expect the
exact form of the data values given here to be used.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_refine_ls_restr.type' refine_ls_restr yes
'_refine_ls_restr_type.type' refine_ls_restr_type yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_refine_ls_restr_type.type' '_refine_ls_restr.type'
_item_type.code line
loop_
_item_examples.case
_item_examples.detail 'p_bond_d'
'bond distance'
'p_angle_d'
'bond angle expressed as a distance'
'p_planar_d'
'planar 1,4 distance'
'p_xhbond_d'
'x-h bond distance'
'p_xhangle_d'
'x-h bond angle expressed as a distance'
'p_hydrog_d'
'hydrogen distance'
'p_special_d'
'special distance'
'p_planar'
'planes'
'p_chiral'
'chiral centers'
'p_singtor_nbd'
'single-torsion non-bonded contact'
'p_multtor_nbd'
'multiple-torsion non-bonded contact'
'p_xyhbond_nbd'
'possible (x...y) hydrogen-bond'
'p_xhyhbond_nbd'
'possible (x-h...y) hydrogen-bond'
'p_special_tor'
'special torsion angle'
'p_planar_tor'
'planar torsion angle'
'p_staggered_tor'
'staggered torsion angle'
'p_orthonormal_tor'
'orthonormal torsion angle'
'p_mcbond_it'
'main-chain bond isotropic thermal factor'
'p_mcangle_it'
'main-chain angle isotropic thermal factor'
'p_scbond_it'
'side-chain bond isotropic thermal factor'
'p_scangle_it'
'side-chain angle isotropic thermal factor'
'p_xhbond_it'
'x-h bond isotropic thermal factor'
'p_xhangle_it'
'x-h angle isotropic thermal factor'
'p_special_it'
'special isotropic thermal factor'
'RESTRAIN_Distances < 2.12'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range less than 2.12 Angtroms.
;
'RESTRAIN_Distances 2.12 < D < 2.625'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range 2.12 - 2.625 Angtroms.
;
'RESTRAIN_Distances > 2.625'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range greater than 2.625 Angtroms.
;
'RESTRAIN_Peptide Planes'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves for peptide planes.
;
'RESTRAIN_Ring and other planes'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves for rings and planes other than peptide planes.
;
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4'
.
save_
###########################
## REFINE_LS_RESTR_TYPE ##
###########################
#
###########################
## proposed new category ##
###########################
#
####################################################
## Submitted by Kim Henrick ##
## Content review by John Westbrook ##
## Kim Henrick approval of changes - Jan 22, 1998 ##
## Editorial review by HB, JW and PMDF ##
####################################################
save_REFINE_LS_RESTR_TYPE
_category.description
; Data items in the REFINE_LS_RESTR_TYPE category record details
about the restraints types used in least-squares refinement.
;
_category.id refine_ls_restr_type
_category.mandatory_code no
_category_key.name '_refine_ls_restr_type.type'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on RESTRAIN refinement for the CCP4 text data set
toxd.
;
;
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
'RESTRAIN_Distances < 2.12' 509 0.005 0.022
'RESTRAIN_Distances 2.12 < D < 2.625' 671 0.016 0.037
'RESTRAIN_Distances > 2.625' 39 0.034 0.043
'RESTRAIN_Peptide Planes' 59 0.002 0.010
'RESTRAIN_Ring and other planes' 26 0.014 0.010
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4' 212 0.106 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6' 288 0.101 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0' 6 0.077 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2' 10 0.114 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4' 215 0.119 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4' 461 0.106 .
loop_
_refine_ls_restr_type.type
_refine_ls_restr_type.distance_cutoff_low
_refine_ls_restr_type.distance_cutoff_high
_refine_ls_restr_type.ebi_U_sigma_wghts
'RESTRAIN_Distances < 2.12' . 2.12 .
'RESTRAIN_Distances 2.12 < D < 2.625' 2.12 2.625 .
'RESTRAIN_Distances > 2.625' 2.625 . .
'RESTRAIN_Peptide Planes' . . .
'RESTRAIN_Ring and other planes' . . .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4' 1.2 1.4 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6' 1.4 1.6 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0' 1.8 2.0 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2' 2.0 2.2 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4' 2.2 2.4 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4' 2.4 . 1.800
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_ls_restr_type.distance_cutoff_high
_item_description.description
; Upper limit of the distance range applied to the current
restraint type.
;
_item.name '_refine_ls_restr_type.distance_cutoff_high'
_item.category_id refine_ls_restr_type
_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__refine_ls_restr_type.distance_cutoff_low
_item_description.description
; Lower limit of the distance range applied to the current
restraint type.
;
_item.name '_refine_ls_restr_type.distance_cutoff_low'
_item.category_id refine_ls_restr_type
_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__refine_ls_restr_type.type
_item_description.description
; This data item is a pointer to _refine_ls_restr.type in the
REFINE_LS_RESTR category.
;
_item.name '_refine_ls_restr_type.type'
_item.category_id refine_ls_restr_type
_item.mandatory_code yes
_item_type.code line
save_
save__refine_ls_restr_type.U_sigma_wghts
_item_description.description
; refine_ls_restr.ebi_U_sigma_wghts is a coefficient used in the
calculation of the weight for thermal parameter restraints in
the program RESTRAIN (see Driessen H, Haneef M I J, Harris G W,
Howlin B, Khan G and Moss D S (1989) J Appl Cryst, 22, 510-516;
and Howlin B, Butler S A, Moss D S, Harris G W and
Driessen H P C (1993) J. Appl. Crystallogr. 26, 622-624.)
The equation used to calculate the actual weight from this
coefficient depends upon the value of _refine_ls_restr.type
-- either "r.m.s. diffs for Uiso atoms at distance *" or
"r.m.s. diffs for Uaniso atoms at distance *".
A similarity restraint is applied to the thermal parameters of
any pair of atoms which are subject to an interatomic distance
restraint (i.e. 1-2 and 1-3 bonded atoms). The thermal
parameter restraints are categorized by the distance between
the two affected atoms. The expected r.m.s. differences in
thermal parameter, either Uiso or Uaniso, are listed for each
shell in _refine_ls_restr.ebi_rmsdev_dictionary.
The weight for the restraint on the thermal parameter difference
between atoms i and j is
w_ij = 1/(s(i)^2 + s(j)^2),
where the calculation of s(i) differs depending upon the value of
_refine_ls_restr.type. If it is equal to "r.m.s. diffs for
Uiso atoms at distance *" its calculation is
s_iso(i) = WU.U_iso(i)^2.
When the type is "r.m.s. diffs for Uaniso atoms at distance *"
its calculation is
s_aniso(i) = WU.d^2,
where d is the interatomic distance and, in both cases, WU is
the value stored in _refine_ls_restr.U_sigma_wghts.
The residual of the restraint is also different in the two cases;
in the isotropic case it is simply the difference between the
U_iso's; in the anisotropic case it is the difference between
the components of the anisotropic tensors along the line joining
the atoms.
See "r.m.s. diffs for Uiso atoms at distance bins" and
"r.m.s. diffs for Uaniso atoms at distance bins" definitions
within _refine_ls_restr.type.
;
_item.name '_refine_ls_restr_type.U_sigma_wghts'
_item.category_id refine_ls_restr_type
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_restr_type.ebi_U_sigma_wghts'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
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