At the Warsaw Congress of the International Union of Crystallography
in 1978, the Data and Computing Commissions of the Union appointed a
working party to propose a standard file structure for
crystallographic data. The working party submitted its report at the
1981 Congress of the Union in Ottawa. The report was adopted by the
Commissions with a recommendation to all authors of crystallographic
programs that they write their programs so that they can read and
write files with this structure. The Standard Crystallographic File
Structure, version of 1981 (SCFS-81), was published in Acta
Crystallographica (1983), A39, 216-224. 
Revised versions
of the format were issued in 1985 and 1987. The text of the 1987
revision to the standard is given below.
c
c Standard Crystallographic File Structure - 87
c ----------------------------------------------
c
c
c This file contains a description of the Standard Crystallogrphic
c File Structure - 87 and is preceeded by a program that will format
c the file for printing on a line printer. The program should be
c detached (and edited if necessary). The rest of the file should
c then be used as an input to this program.
c
c
Program Scfspt
c
c A PROGRAM FOR FORMATING THE SCFS MANUAL FOR PRINTING
c ----------------------------------------------------
c This program is designed to format the SCFS Description manual for printing.
c Separate this section of code from the main file, make the necessary
c changes to the OPEN and CLOSE statements for your machine, compile and
c run the program. The output will be formated for printing.
c
Character*80 Line
Character*4 Form
Data Form /''/
l=1
Open(unit=13,file='SCFS87.MAN',status='OLD')
Open(unit=14,file='SCFS87.LIS',status='NEW')
100 Read(Unit = 13, Fmt ='(A80)', End = 200) Line
if (Line(1:4).eq.Form) then
l=l+1
Write(Unit = 14, Fmt ='(''1'',59X,I3,/)') l
else
Write(Unit = 14, Fmt = '(20X,A80)' ) Line
endif
Go to 100
200 Write(Unit = 14, Fmt = '(''1''//)')
Close(unit=13)
Close(unit=14)
Stop
End
-- SCFS-87 --
STANDARD CRYSTALLOGRAPHIC FILE STRUCTURE-87 2
(Supersedes SCFS-84) 2
* The original version of this standard together with background information
on its purpose and philosophy was published in Acta Cryst. (1983) A39, 216-224
as SCFS-81. A second version (SCFS-84) became available in 1985 (Acta Cryst. 2
(1985) A41, 399). 2
* Changes introduced in SCFS-84 are indicated by '1' in the right hand margin 1
Changes introduced in SCFS-87 are indicated by '2' in the right hand margin 2
Approved by the Data and Computing Commissions
of the International Union of Crystallography
Project Coordinator: Dr. I. D. Brown
Institute for Materials Research
McMaster University, Hamilton
Ontario, Canada, L8S 4M1
NetNorth Network Address "1002332@MCMASTER"
A program to read data in the SCFS87 format may be obtained from
Dr H.D.Flack, University of Geneva, Switzerland ([email protected])
Contents Contents
C O N T E N T S
---------------
1. Introduction
2. Transfer Medium
3. Data Structure
4. Formats
Sections required for file management (must be present)
4.1.1 TITLE
4.1.2 END
Sections giving commonly used crystallographic data
4.2.1 CELL DIMension
4.2.2 SG NAME Space group symbol 1
4.2.3 SYMMETRY Space group symmetry operators
4.2.4 ATOMS Atomic coordinates and other atomic data 1
4.2.5 FORM FACtor Atomic scattering factors
4.2.6 HKL Structure factors, powder patterns
4.2.7 CONDITIOns Experimental conditions
4.2.8 FORMULA Chemical formula
4.2.9 REFERENCe Literature citations
4.2.10 REMARK Unstructured text
4.2.11 BONDS List of bonds 1
4.2.12 CONNECTIon Interatomic connections 2
4.2.13 CRYSTAL Crystal parameters 2
4.2.14 COMMENTS Structured text 2
Sections giving the basic data in compact form
4.3.1 ATOM COOrdinates
4.3.2 HKL PACK Structure factors
Sections of interest to protein crystallographers
4.4.1 ATOM MACromolecule Atomic coordinates
4.4.2 ORTHOGONal Transformations for atomic coordinates
4.4.3 HKL PROTein Structure factors
4.4.4 ANIS MACromolecule Anisotropic atomic displacement parameters 2
4.4.5 CONN MACromolecule Connectivity 2
Sections defined in earlier standards and now superseded
4.10.1 SPACE GRoup 1
4.10.2 ATOM 1
4.10.3 CONDITIOns:blank 2
4.10.4 FORM FACtor:blank 2
5. Appendix I -- Sample of a Standard Crystallographic File
1.Introduction Introduction 1.
Standard Crystallographic File Structure-87
-------------------------------------------
1. Introduction
The purpose of the Standard Crystallographic File Structure is to 1
assist in the exchange of crystallographic data between laboratories and to 1
make it easy for the same data to be used as input to different programs. It 1
is expected to be the standard used by the journals of the International Union1
of Crystallography when they are ready to accept papers in machine readable 1
form. The present version is capable of containing the complete text of a 2
paper as well as all the information normally required by Acta Cryst. C 2
for the publication of a crystal structure. 2
The File Structure has been designed to include all types of 1
crystallographic data, to be compatible with all types of computers, to be 1
easy to program for both reading and writing and to give a listing that is 1
easy to read visually. 1
Since there are many possible uses to which such a file may be put 1
(e.g. transfer of protein structures or the archiving of mineral powder 1
patterns), the only information that must be included in the file is that 1
needed for file management. With a few exceptions, the absence of a datum 1
from a particular field implies that the datum was not available or was not 1
needed for the present purpose. 1
The file structure has been designed to allow for extension to new 1
types of data as the need arises. Anyone who has needs that are not met by 1
the current standard is invited to contact the project coordinator whose name 1
appears on the title page.
This standard supersedes the SCFS-81 standard published in Acta Cryst. 1
(1983) A29, 216-224 and the SCFS-84 standard (Acta Cryst. (1985) A41, 399) 2
2. Transfer Medium
The file may be transferred by any acceptable medium. Unless otherwise
specified by the user, the following conventions will be assumed (some common
alternatives are included in parentheses).
Cards
Standard 80 column IBM cards punched using the 029 (026) punch convention.
Magnetic Tape
9 track, 800 bits per inch (9 track 6250 or 1600 bpi or 7 track 800 bpi). 2
Unlabelled. USASCII/7 (EBCDIC): 80 characters/record; 45 records/block,
blank filled if necessary (unblocked).
3. The Data Structure of a Standard Crystallographic File
For simplicity, the file is described in terms of card images but without
implying that it must physically exist in the form of cards. A sample file is
given in Appendix I.
3.1 Data Structure Data Structure 3.1
3.1 A file consists of entries, each entry being logically independent of
other entries. An entry normally will consist of data referring to one
crystalline phase. Each entry begins with a TITLE card and ends with an
END card.
3.2 An entry consists of a number of sections each including data of a
particular type, e.g. atomic coordinates or structure factors. Each
section begins with a Header Card and ends with an End of Section (EOS)
Card (any card with * in col.1). The End of Section card ensures that
the program is ready to read the next card as a Header.
3.3 Each section consists of formatted cards (or lines) containing 80
characters (including blanks). 5 characters at the end of each card are
reserved for card sequence numbers. Sequence numbers should be integers 1
(I5) and, if used, should be arranged so that the cards in the entry are 1
in the correct order when sorted on increasing value of the sequence 1
number. 1
3.4 The character set is restricted to upper and lower case letters, numbers1
and ASCII symbols between 20 HEX (' ') and 7A HEX ('z') inclusive but users 1
are reminded that the 46 characters 0-9 A-Z , . + - * / ( ) = blank are the 1
only ones available on all machines. Numbers are expressed as integers 1
or real numbers using FORTRAN conventions, that is a decimal point appearing 1
in a real number takes precedence over the format as given, if no decimal 1
point is given, one is assumed according to the format specification. 1
To avoid confusion, it is recommended that the decimal point be included 2
except for Fn.0 formats where integers are acceptable. If a number is 2
too large or too small to fit into the field, the optional E format may be 2
used as this can be read in FORTRAN using an F format. 2
3.5 Cards are of two types:
(a) Header Cards are used to start a new section. The first 8
characters indicate the format of the following data cards and in some
cases the information that is to be found on them. In addition,
each header card may contain comments, such as alphanumeric column
headings to help visual reading (see Appendix I).
(b) Data Cards contain the data specified by the most recently read
header card. An asterisk (*) in column 1 indicates the last card in
the section.
3.6 Most data cards begin with the following three fields:
(a) EOS (End of Section) Col. 1
This must be an asterisk (*) on the last card of each section,
otherwise any other legal character (normally blank) may appear in
this field. The end-of-section card may be a normal data card but
in sections with a card identifier a special end of section card may
be used containing *EOS in columns 1-4 and columns 5-75 blank.
3.6 Data Structure Data Structure 3.6
(b) CID (Card Identifier) Col 2-5
Within each section, the format of all the data cards is the same
but in most sections the type of information stored on the card may
be different. In these sections, each card contains a card identifier
(CID) whose value determines the type of information carried
(e.g. in the HKL section, the value of CID will determine whether
the card contains intensities, calculated structure factors or
powder data). CID uses an A4 field and is left justified. The last
card of any section may have "EOS " as a card identifier. No other
data should appear on a card with CID = "EOS ".
(c) DSK (Data Set Key) Cols. 6-9
Most cards also include a Data Set Key (DSK) which allows the user
to associate different data together. For example, the user may
wish to include data from several experiments in the same entry
(e.g. data from x-ray and neutron diffraction experiments, or data
for a native protein and several of its isomorphs). Cards from the
different experiments would carry different values of DSK but could
appear together within the same section (e.g. the structure factors
of several isomorphs for a given reflection can be grouped
together). DSK may contain any legal characters chosen by the user.
Any card on which DSK is blank is assumed to contain data that
applies to all the data sets included in the entry.
3.7 Header cards that cannot be interpreted are to be ignored. Some
consequences are:
i) Blank cards may be used to separate sections for visual effect.
ii) The presence of an incorrect header may result in problems during
reading of the file since cards will be ignored until an interpretable
header is found.
iii) Instruction or data cards for a user's program can be added to a
file provided they do not mimic legal header cards. This can be
ensured by using a character other than a letter or blank in columns
1-8.
iv) Comments can be inserted between sections providing that columns 1-8
do not mimic header cards (e.g. if they are left blank). Unlike
comments included in the COMMENTS or REMARK section, these comments may not 2
be read by a user's program and should be used with care.
3.8 Data cards that cannot be interpreted should be avoided. Since these
will be read with a fixed format read statement, they could cause a fatal
read error. Fields that are undefined in the present standard should be 2
left blank as these may be defined in future releases. 2
3.9 Sections may follow each other in any order, and the same section may be
included any number of times within an entry but where the file contains
duplicate information (e.g. two sets of cell dimensions) the values
appearing latest in sequence are the values to be used.
3.10 Data Structure Data Structure 3.10
3.10 No default values are assumed except where noted below. If a field 2
is blank, it is assumed that the data is not available or not required. 2
However, most computers will read a blank numeric field as zero. Where 2
this is likely to be confused with a non-defaulted value of zero, provision 2
is made for a defaulted field to be indicated in a different manner, usually 2
by filling it with '9's. 2
3.11 When writing a program to read a standard file it is only necessary to 1
arrange to read those sections that contain data needed by the program. 1
If the program is written to ignore any header cards that it does not 1
recognise, all the cards in an unrecognised section will be automatically 1
skipped. Only when a recognised header is once again encountered will 1
the program resume reading data. Care should be taken to check for 1
defaulted numeric fields, particularly those that are set to their 1
maximum value. 1
3.12 When writing a program to write a standard file it is only necessary to 1
arrange to write sections for which data are available. In many cases a 1
defaulted value can be written as zero but in cases where the parameter 1
being defaulted might legitimately have the value of zero (e.g. h, k 1
or l) the field defaulted should be given the maximum value allowed by 1
the format (e.g. see section 4.3.2 below). 1
4. Formats for the Standard Crystallographic File Structure-87
--------------------------------------------------------------
Each section starts with the Header Card shown. The first eight
characters are reserved for an alphabetic section name. Otherwise the card may
contain any alphanumeric characters. All the other cards in the section
are data cards and have the format shown. The last card in each section must
have an asterisk in column 1. Columns 76-80 on all cards are reserved for a
card or line sequence number. The TITLE and END cards must appear in all
entries. Other sections may be included as required by the user. Unless
otherwise stated, all microscopic dimensions (a,b,c,lambda) are in Angstrom
units, all macroscopic dimensions are in mm, all angles in degrees and
temperatures in Kelvin.
------------------------------------------------------------------------------
******************************************************************************
4.1 SECTIONS REQURIED FOR FILE MANAGEMENT 4.1
******************************************************************************
------------------------------------------------------------------------------
*****************************
4.1.1 TITLE (A1, A66, A8)
*****************************
This must be the first card of any entry.
Col. Format
1 A1 EOS * This section may only contain 1 card and must
therefore have an asterisk in column 1.
2-67 A66 Name of compound or other identification.
Use only one card.
This information may also be repeated in columns
9-75 of the header card to allow visual
identification of a card deck.
Chemical names may also be given in the COMMENTS 2
section (4.2.14). 2
68-75 A8 Entry code chosen by the user to distinguish
different entries in a multi-entry file. This
field allows the user to identify and select
the entry in which he or she is interested. Any
legal characters are allowed in this field.
A TITLE card will start a new entry only at the beginning of the file 1
or immediately following an END section. A TITLE section occurring in any 1
other position will presumably overwrite the title in the current entry. 1
*************
4.1.2 END
*************
This must be the last card of any entry. No data cards follow the END
header.
-------------------------------------------------------------------------------
*******************************************************************************
4.2 SECTIONS GIVING COMMONLY USED CRYSTALLOGRAPHIC DATA 4.2
*******************************************************************************
-------------------------------------------------------------------------------
*************************************************
4.2.1 CELL DIMension (A1, 2A4, 1X, 6F10.4, F5.0)
*************************************************
Col. Format
1 A1 EOS * on the last card of the section.
2-5 A4 CID Card Identifier:CELL(or blank),ERRS,VOL,PHYS or EOS 2
6-9 A4 DSK Data Set Key(see section 3.6(c))
10 1X
11-20 F10.4 x1 | 2
21-30 F10.4 x2 | 2
31-40 F10.4 x3 |Parameters whose value depends on the CID 2
41-50 F10.4 x4 | (see below) 2
51-60 F10.4 x5 | 2
61-70 F10.4 x6 | 2
71-75 F5.0 x7 | 2
CID Value of parameter
--- ------------------
CELL Cell dimensions. The use of CELL is recommended in preference to blank2
or blank
x1 A |Unit cell lengths in Angstrom units. All values must
x2 B |be given. This unit cell must correspond to the
x3 C |setting given in SG NAME (Section 4.2.2)
x4 ALPHA |
x5 BETA |Unit cell angles in degrees. All values must be
x6 GAMMA |given.
x7 Z The number of the formula units given in the FORMULA
section (4.2.8) contained in the unit cell given here.
ERRS x1-x6 Errors in the corresponding cell constants given above
VOL Cell Volume and related data 2
2
x1 VOL Volume of unit cell (cubic Angstroms) 2
x2 EVOL Error in volume of unit cell 2
x3 FW Formula weight contained in VOL/Z 2
-3 2
x4 DC Calculated density (mg.mm ) 2
x5-x7 Undefined 2
2
PHYS Physical measurements concerning the unit cell 2
-3 2
x1 DM Measured density (mg.mm ) 2
x2 SIG(DM) Standard error in density 2
x3 TEMP(DM)Temperature of density measurement 2
x4-x7 Undefined 2
EOS End of section. No data given on this card.
*******************************************
4.2.2 SG NAME (A1, 2A4, 1X, A24, 3I5, 26X) SG NAME 4.2.2 2
******************************************* 1
1
1
Col. Format 1
1
1 A1 EOS * on the last card of section 1
2-5 A4 CID Card Identifier: LATT, HERM, HALL, SCHN, SYST 2
or EOS. 2
6-9 A4 DSK Data Set Key (see section 3.6(c)) 1
10 1X 1
11-34 A24 SG Space group name or other data in appropriate 1
form (depending on CID) 1
35-39 I5 i1 | 2
40-44 I5 i2 | Parameters whose value depends on CID 2
45-49 I5 13 | 2
50-75 26X Undefined 1
1
1
CID Value of parameter 1
--- ------------------ 1
1
LATT Parameters to be used in conjunction with the symmetry operators 2
listed in the SYMMETRY section (4.2.3) 2
2
11 A1 CENT 'C' or '-' if there is a center of symmetry 2
at the origin 2
'N' or '+' if there is no center of symmetry2
at the origin. If CENT is blank 2
'N' is assumed 2
12 A1 LT Lattice type (P,A,B,C,F,I,H or R). 2
Use H or R for the hexagonal setting of a 2
rhombohedral space group, P for the 2
rhombohedral setting 2
If LT is blank 'P' is assummed 2
35-39 I5 i1 NS Number of symmetry operators other than 2
those involving inversion through the 2
origin and lattice centering operations 2
40-44 I5 i2 MS MS*NS = number of symmetry operations 2
required to generate the contents of the 2
unit cell given in the CELL section 2
45-49 I5 i3 Number of symmetry matrices having an 2
identical pattern of zeros 2
2
NOTE: The LATT card is to be used in conjunction with the 2
the SYMMETRY section (4.2.3). The full set of symmetry 2
operators can be generated by multiplying each of those listed 2
in the SYMMETRY section by the inversion operator if 2
CENT = 'C' or '-' and adding the translations indicated 2
by LT to the results. 2
If all the symmetry operators are given explicitly in the 2
SYMMETRY section (as might be required if the CONNECTION 2
section (4.2.12) is used) the LATT card is not required. 2
4.2.2 SG NAME SG NAME 4.2.2
2
HERM 11-22 A12 SG Hermann-Mauguin space group symbol for the 1
setting actually used (see note below). 1
23-26 A4 X0 |Origin shift in the form 1/8 -3/8 1/4 etc. 1
27-30 A4 Y0 |(4 characters per axis, right justified). 1
3l-34 A4 Z0 |This describes a vector from the 1
|origin given in the standard 1
|(International Tables) setting to the 1
|origin of the cell used in the 1
|description of the structure. The 1
|axis system in which the vector is 1
|given is that defined in the field SG 1
|above. 1
35-75 41X Undefined. 1
1
HALL Hall space group symbol for the setting used as described in 1
Acta Cryst. A37 517-525 (1981). Note: use only upper case 1
letters, the minus sign preceeds the character it refers to, 1
leave a space before each rotation symbol (i.e. between 1
character groups belonging to different axes), superscripts 1
immediately follow the number, subscripts follow superscripts 1
(if given), e.g. -P 2YN; -P 2AC 2N; P -2 2. 1
This form of the space group symbol is designed to be machine 2
interpretable and can be used to define unambiguously the choice 2
and setting of any space group. 2
SCHN Schoenflies symbol. Give subscript first followed by slash and 1
3 1
superscript e.g. C = C4H/3 1
4h 1
SYST Crystallographic system = TRICLINIC or ANORTHIC 2
MONOCLINIC 2
ORTHORHOMBIC 2
TETRAGONAL 2
TRIGONAL 2
HEXAGONAL 2
RHOMBOHEDRAL 2
or CUBIC 2
EOS End of section. No data given on this card. 1
1
Note: If there is a discrepancy between the space group symbol
and the operators given in the SYMMETRY section, the
SYMMETRY section takes precedence.
4.2.2 SG NAME SG NAME 4.2.2
Note on the Definition of the Hermann-Mauguin Space Group Symbols
-----------------------------------------------------------------
It is not possible to calculate the symmetry operators unambiguously from
the traditional Hermann-Mauguin symbol for all possible settings. The
following set of rules for writing Hermann-Mauguin symbols is designed
to remove this ambiguity and is compatible with a number of currently used
programs that generate symmetry operators from the space group symbol.
Alternatively the symmetry operators may be given explicitly in the SYMMETRY
section (4.2.3) or the Hall space group symbol corresponding to the setting
used may be given. The latter is recommeded since the Hall symbol has been
explicitly designed for computer use. Care should be taken in writing the
Hermann-Mauguin symbol to ensure that it is compatible with the programs
that will be used to read it.
Give the symbol in the short form given in International Tables for
(X-Ray) Crystallography Volume I or Volume A with the following conventions.
l. Left justify the space group symbol.
2. Leave a space after the lattice type.
3. Leave a space between the symmetry symbols referring to the different
directions.
_
4. Write 4 as -4 etc.
5. Write 2 as 21 etc.
1
6. Where alternative standard settings are given in International Tables the
following conventions are assumed:
(a) For monoclinic space groups the b axis setting is assumed unless
otherwise indicated, e.g.:
P 21/N = P 1 21/N 1 (b axis setting)
P 1 1 21/N (c axis setting)
P 21/N 1 1 (a axis setting)
(b) In centrosymmetric space groups the setting with the origin at a
center of symmetry is assumed unless an origin shift is given in
columns 23-34.
(c) For rhombohedral space groups the setting depends on the form in
which the CELL DIMensions are given.
7. If the Hermann-Mauguin symbol is not the same as that given in
International Tables, a cyclic permutation of axes is assumed in any case
where there is an ambiguity e.g. P2 22. Other permutations can be
1
achieved through an origin shift.
8. Any other setting can be obtained by a suitable shift of the origin as
given in columns 23-34.
**************************************************************** 2
4.2.3 SYMMETRY (A1,2A4,A1,2(3I2,F10.7,4X),3I2,F10.7,A3,2I2,2X) 4.2.3 2
**************************************************************** 2
Col. Format
1 A1 EOS * on the last card of the section
2-5 A4 CID Card Identifier: SYOP (or blank), SPOS, TWIN or EOS 2
6-9 A4 DSK Data Set Key (see section 3.6(c))
10 A1 a1 | 2
11-12 I2 W11 |
13-14 I2 W12 |
15-16 I2 W13 |
17-26 F10.7 w1 |
27-30 4X | Parameters whose value depends on the
31-32 I2 W21 | CID
33-34 I2 W22 |
35-36 I2 W23 |
37-46 F10.7 w2 |
47-50 4X |
51-52 I2 W31 |
53-54 I2 W32 |
55-56 I2 W33 |
57-66 F10.7 w3 |
67-69 A3 a2 | 2
70-71 I2 i1 | 2
72-73 I2 i2 | 2
74-75 2X 2
W and w define a Seitz matrix of the following form: 2
The transformed coordinates (x',y',z') are related to those (x,y,z)
given in the ATOMS cards (x,y,z) by
x' = W11.x + W12.y + W13.z + w1
y' = W21.x + W22.y + W23.z + w2
z' = W31.x + W32.y + W33.z + w3
CID Value of parameters
--- -------------------
SYOP Used for giving the symmetry operators of the space group. 2
or blank The use of SYOP is recommended in place of blank 2
NOTE: The SG NAME:LATT (section 4.2.2) is used in conjunction 2
with this section. 2
If either CENT or LT is given in SG NAME:LATT 2
the corresponding symmetry operators should NOT be given here 2
If operators are used in the CONNECTIon section (4.2.12) it 2
may be necessary to give all operators explicitly 2
a1 Undefined
W and w Seitz matrix for a symmetry operator
4.2.3 SYMMETRY SYMMETRY 4.2.3
a2 ASYM User defined symmetry operator identifier corresponding 2
to that used in the CONNECTIon section (4.2.12) 2
In the event that the symmetry operators are generated 2
algorithmically, these identifiers may be sequence 2
numbers in an ordered list of operators generated by 2
the algorithm. In this case it may be useful to use 2
the COMMENTS:SYOP section (4.2.14) to specify the 2
algorithm used. 2
i1-i2 Undefined
In the event of a disagreement between the SG NAME and SYMMETRY
sections, the information in the SYMMETRY section will be assumed
correct. The operators given here must correspond to the unit cell
given in CELL DIMensions (Section 4.2.1) and the coordinates given in
ATOMS (Section 4.2.4), ATOM COOrdinates (Section 4.3.1) or ATOM 1
MACromolecule (Section 4.4.1). They must also correspond to the values 2
given for CENT and LT in SG NAME:LATT (Section 4.2.2) 2
2
SPOS Used for giving coordinates of special positions
2
a1 WYCK Wyckoff letter of the special position 2
W and w The coordinates of the special position expressed as 2
a Seitz matrix so that x',y',z' are the coordinates 2
of the special position and x,y,z are free variables. 2
a2 ASPS User defined identifier for the special position 2
See note on ASYM above. The algorithm used may be 2
given in the COMMENTS:SPOS section (4.2.14) 2
i1 MULT Multiplicity of the special position 2
i2 Undefined 2
2
TWIN Used for specifying twin relationships 2
2
a1 Undefined 2
W If the coordinates in the crystal are x,y,z the 2
coordinates in the twin component are x',y',z' 2
Note that the matrix that transforms the Miller indices 2
is the transpose of W 2
w Undefined 2
a2 ATWIN User defined twin identifier (see the CRYSTAL:TWIN 2
section (4.2.13)) 2
i1 Undefined 2
i2 Undefined 2
EOS End of section. No data given on this card.
************************************************************* 1
4.2.4 ATOMS (A1, 2A4, A2, A6, 6F8.5, I3, A1, 1X, A4, I1) ATOMS 4.2.4 1
************************************************************* 1
1
1
Col. Format 1
1
1 A1 EOS * on the last card of section. 1
2-5 A4 CID Card Identifier: ATCO, ATCE, UALL, UALE, 2
UIJ, UIJE, CHEM, BETA, BIJ, BETE, BIJE, 2
or EOS. 1
6-9 A4 DSK Data Set Key (see section 3.6(c)) 1
10-11 A2 AN atom name, |These fields are used 1
normally an |to associate data which 1
element symbol |appear on different cards 1
left justified. |but refer to the same atom. 1
(Iodine = I |AN can be any omitted if 1
not J) |only ATCO cards are used and 1
|AT is given. If more than 1
12-17 A6 AI atom identifier, |one ATOMS card refers to the 1
any legal |same atom (e.g. ATCO and 1
characters. |ATCE) then AN (and AI if 1
|necessary) must be given. 1
18-25 F8.5 x1 | 1
26-33 F8.5 x2 | 1
34-41 F8.5 x3 | 1
42-49 F8.5 x4 |Parameters whose value depends on CID 1
50-57 F8.5 x5 |(see below) 1
58-65 F8.5 x6 | 1
66-68 I3 i1 | 1
69 A1 a1 | 1
70 1X | 1
71-74 A4 a2 | 1
75 I1 i2 | 1
1
The cards may be grouped in any order, e.g. they may be ordered by CID 1
or by AN and AI. The characters in columns 10-17 must be the same on 1
all cards referring to the same atom. 1
4.2.4 ATOMS ATOMS 4.2.4
1
CID Values of Parameters 1
--- --------------------
ATCO atomic coordinates
x1 x |Atomic coordinates
x2 y |in fractions of unit cell
x3 z |
x4 U For i2 = 1, isotropic atomic displacement parameter 2
2 2 1
T = exp(-8(PI) U (sin(THETA)/LAMBDA) ). 1
For i2 = 2, isotropic atomic displacement parameter 2
equivalent to the anisotropic one. 2
x5 OCC occupation number 1
The occupation number is only physically 1
meaningful if 0.LT.OCC.LT.1. In cases where 1
this parameter is refined it may, within the 1
limits of error, lie outside this range. If 1
this field is blank a value of 1.0 is assumed. 1
To avoid possible reading problems it would be 1
better to use a small non-zero value in cases 1
where an occupation number of 0.0 is 1
intended. 1
1
x6 OXID Ionic charge or formal oxidation state 1
i1 Wyckoff position multiplicity (.GT.1)
a1 Wyckoff position letter
a2 AT Atom type. Any four characters used to define the form
factor (see Section 4.2.5) or other atomic property, 2
e.g. in molecular graphics to indicate the colour 2
assigned to an atom in a molecular diagram 2
i2 DT Atomic displacement parameter type
1 = isotropic
2 = anisotropic
0 or 9 = default
8 = overall (value supplied on ATOMS:UALL)
ATCE errors in atomic coordinates
x1 SIGMA(x) | N.B. If these are written as integers (I8)
x2 SIGMA(y) | they will be read as errors in the
x3 SIGMA(z) | fifth decimal place.
x4 SIGMA(U) |
x5 SIGMA(OCC) |
i1 Undefined
a1 Undefined
a2 ASPS Special position identifier as used in SYMMETRY:SPOS 2
section (4.2.3). Use only the left hand 3 characters 2
4.2.4 ATOMS ATOMS 4.2.4
UALL overall isotropic atomic displacement parameter 2
2
AN Undefined 2
AI Undefined 2
x1 U(overall) 2
x2-i2 Undefined 2
2
UALE standard error in UALL 2
1
UIJ anisotropic atomic displacement parameters (U form). This is the 1
recommended form. 1
x1 U(11) |
x2 U(22) | as used in the expression
x3 U(33) | 2
x4 U(12) | T = exp(-2(PI) (& & U(ij)h h a*a*))
x5 U(13) | i j i j i j
x6 U(23) |
UIJE error in UIJ
CHEM Gives chemical properties of the atom 2
2
x1 CN Coordination number (as defined by the CONNECTIon section 2
(4.2.12) but including the attached H atoms given in x2 2
x2 NH Number of attached H atoms that are not included in the 2
CONNECTIon section (4.2.12) 2
x3 Formal charge (in electrons) 2
x4 Physical charge (in electrons) as determined by calcul- 2
ation, electron summation etc. Give details in REMARK 2
section (4.2.10) if necessary 2
x5 x x for 2D diagram 2
x6 y y for 2D diagram 2
i1 GRP Group number. A group is any collection of atoms defined 2
by the user 2
a1 Chirality flag. R or S using the definition of Cahn, 2
Ingold and Prelog 2
a2 (Field reserved for macromolecular subunit) 2
i2 CMP Component number. A component is any group of atoms which 2
form a connected set according to the data given in the 2
CONNECTIon section (4.2.12) 2
4.2.4 ATOMS ATOMS 4.2.4
2
The use of UIJ and UIJE is preferred to the use of the following four CID's 2
-------------------------------------------------------------------------- 2
BETA anisotropic atomic dispacement parameters (Beta form)
x1 BETA(11)|
x2 BETA(22)| as used in the expression
x3 BETA(33)| T = exp(-(& & BETA(ij)h h )
x4 BETA(12)| i j i j
x5 BETA(13)|
x6 BETA(23)|
BIJ anisotropic atomic displacement parameters (B form)
x1 B(11) |
x2 B(22) | as used in the expression
x3 B(33) | T = exp(1/4(& & B(ij)h h a*a*))
x4 B(12) | i j i j i j
x5 B(13) |
x6 B(23) |
BETE | standard errors in the values given on
BIJE | BETA and BIJ cards
EOS End of section. No data given on this card.
********************************************
4.2.5 FORM FACtor (A1, 2A4, A2, A4, 6F10.6) FORM FACtor 4.2.5
********************************************
The form factor can be given in different ways according to the value of
CID.
Col. Format
1 A1 EOS * on the last card of the section
2-5 A4 CID Card Identifier: TABL, EXP1, EXP2 or EOS 2
For FORM FACtor:blank see section 4.10.4 2
6-9 A4 DSK Data Set Key (see section 3.6(c))
10-11 A2 AN Atom name (may be blank if AT is given)
12-15 A4 AT Atom type (may be blank if AN is given. If
both AN and AT are given they must both agree
with the values given on the ATOMS card).
16-25 F10.6 x1 |
26-35 F10.6 x2 |
36-45 F10.6 x3 |
46-55 F10.6 x4 | Parameters whose value depends on CID (see
56-65 F10.6 x5 | below)
66-75 F10.6 x6 |
CID Values of Parameters
--- --------------------
TABL Table of atomic scattering factors 2
2
x1 sin(THETA)/(LAMBDA)| one card needed for each value of 2
x2 f | sin(THETA)/(LAMBDA) for each type of 2
x3 f' | atom as specified by AN and/or AT 2
x4 f" | Note that f' may be included in x2 (in 2
| which case x3 = 0.0) or it may be 2
| given in x3 ( in which case it should 2
| not be included in x2) 2
EXP1 Analytical form of atomic scattering factor
x1 a1 |
x2 b1 |
x3 a2 |
x4 b2 |
x5 a3 | two cards (EXP1 and EXP2) needed for
x6 b3 | each element or atom type.
|
EXP2 x1 a4 | Parameters are used in the expression
x2 b4 | given below (see (International Tables
x3 c | for X-ray Crystallography IV, p. 71).
x4 f' |
x5 f" |
4 2
form factor = & a exp(-b (sin THETA/LAMBDA) ) + c + f' + if"
j=1 j j
EOS End of section. No data given on this card.
4.2.5 FORM FACtor FORM FACtor 4.2.5
Form factors can be identified with atoms in one of two ways: either
through AN (normally an element symbol) or through AT (atom type). If
both are given in this section both must agree with the values of AN and
AT given in ATOMS (Section 4.2.4). For neutron scattering lengths the
EXP form can be used with a = b = 0 and c = scattering length in
-15 j j
fm(=10 m).
*****************************************
4.2.6 HKL (A1, 2A4, 3I5, A1, 5F10.3) HKL 4.2.6
*****************************************
This section contains information on Bragg reflections.
Col. Format
1 A1 EOS * on the last card of the section
2-5 A4 CID Card Identifier: FOBS (or blank), FSQR, INT, CALC, 2
PWDR, ANGL, ISOM or EOS 1
6-9 A4 DSK Data Set Key (see section 3.6(c))
10-14 I5 h |
15-19 I5 k | Miller indices of the reflection
20-24 I5 l |
25 A1 a flag: A, blank, 0 or 1 = normal reflection, 1
B or 2 = unobserved reflection, 1
C or 3 = unreliable measurement, 1
D or 5 = space group systematic absence 1
The use of letters is recommended to improve 1
the legibility of the listed file. 1
26-35 F10.3 x1 |
36-45 F10.3 x2 | Parameters whose values depend on CID
46-55 F10.3 x3 | (see below)
56-65 F10.3 x4 |
66-75 F10.3 x5 |
CID Values of Parameters
--- --------------------
FOBS to report observed structure factors only 2
or blank The use of FOBS instead of blank is recommended. 2
x1 |F(obs)| Observed structure factor
x2 SIGMA(|F(obs)|) Standard error in |F(obs)| (normally derived
from counting statistics).
x3-x5 Undefined
2 2
FSQR to report |F| 2
2 2
x1 |F(obs)| 2
2 2
x2 SIGMA(|F(obs)| ) 2
2 2
x3 |F(calc)| 2
x4-x5 Undefined 2
INT to report intensity measurements
x1 |F(obs)| | See above.
x2 SIGMA(|F(obs)|) |
x3 I(net) Observed intensity corrected for background
but not absorption, extinction, etc.
x4 I (background) I(observed) = I(net) + I(background)
x5 SIGMA(I(net)) Standard error in I(net) (normally derived
from counting statistics).
4.2.6 HKL HKL 4.2.6
CALC to report calculated structure factors
x1 |F(obs)| | See above
x2 SIGMA(|F(obs)|) |
x3 |F(calc)| Modulus of calculated structure factor
x4 A | F(calc) = A + iB
x5 B |
PWDR to report powder patterns
x1 I(obs) Uncorrected intensity
x2 SIGMA (I(obs)) Standard error in I(obs)
x3 2(THETA) (degrees)
x4 SIGMA(2(THETA)) Standard error in 2(THETA)
ANGL To report diffractometer setting angles
x1 2(THETA) | Diffractometer angles used for measuring this 1
x2 OMEGA | reflection according to manufacturer's 1
x3 CHI or KAPPA | definition. Give diffractometer make and 1
x4 PHI | definition of the angles OMEGA, CHI or KAPPA, 1
x5 PSI | PHI, and PSI on a COMMENTS:ANGL (section 4.2.14)2
| card. See also the CONDITIOns:HKL, ORNT or OUB11
| section (4.2.7) 1
ISOM to report data from isomorphs (e.g. of macromolecules)
x1 |F(obs)| | see above
x2 SIGMA(|F(obs)|) |
x3 |F(calc)| | Amplitude and phase (degrees) due to
x4 ALPHA(c) | isomorphous modification
2 ___ 2 2 ___
x5 g=(SIGMA(|Fo(hkl)|-|Fo(hkl)|))/(SIGMA(|Fo(hkl)|)+SIGMA(|Fo(hkl)|))
Structure factors for different isomorphs should use a different
value for DSK but cards may be ordered within a section by hkl
e.g. CID DSK h k l
ISOM IS3 3 4 -5
CALC NATV 3 4 -6
ISOM IS1 3 4 -6 + data
ISOM IS2 3 4 -6
ISOM IS3 3 4 -6
CALC NATV 3 4 -7
etc.
EOS End of section. No data given on this card.
******************************************
4.2.7 CONDITIOns (A1, 2A4, A1, 6F10.0, 5X) CONDITIOns 4.2.7
******************************************
This section is used to describe the conditions of measurement. Together 2
with the COMMENTS section (4.2.14) it contains 2
the majority of the items required by Acta Crystallographica for the 2
publication of a crystal structure determination (Acta Cryst. C41 (1985),1-4) 2
Col. Format
1 A1 EOS * on the last card of the section
2-5 A4 CID Card Identifier: CELL, INT, HKL, STD, ABS, FACE, 2
FARE, ORNT, OUB1, OUB2, EQIV, REFN, STAT, VAR or EOS2
(for CONDITIOns:blank, see 4.10.3) 2
6-9 A4 DSK Data Set Key (see section 3.6(c))
10 A1 a |
11-20 F10.0 x1 | Parameters whose value depends on CID
21-30 F10.0 x2 | Note that the parameters (x1-x6) may be
| written as integers and will be correctly read
31-40 F10.0 x3 | by an F10.0 format. Other formats (e.g.
| F10.5) may be written and will also be
41-50 F10.0 x4 | correctly read if the decimal point is
| included.
5l-60 F10.0 x5 |
61-70 F10.0 x6 |
71-75 5X undefined
CID Value of Parameters
--- -------------------
CELL Conditions used for measuring the unit cell dimensions 2
a RAD Radiation used for measuring unit cell 2
N = neutrons 2
E = electrons 2
X = X-rays 2
S = synchrotron radiation 2
x1 LAMBDA Wavelength used to measure unit cell (Angstroms) 2
x2 TEMP Temperature at which cell was measured (K) 2
x3 2THETAMIN Minimum 2*theta used in measuring cell (degrees) 2
x4 2THETAMAX Maximum 2*theta used in measuring cell (degrees) 2
x5 NCELL Number of reflections used in measuring the cell 2
x6 Undefined 2
2
INT Conditions used for measuring the intensities 2
a RAD Radiation used for measuring intensities (see CELL) 2
x1 LAMBDA Wavelength used to measure intensities (Angstroms) 2
x2 TEMP Temperature at which the intensities were 2
measured(K) 2
x3 ST/LMIN Minimum sin(theta)/lambda at which intensities were 2
measured 2
x4 ST/LMAX Maximum sin(theta)/lambda at which intensities were 2
measured 2
x5 NINT Total number of reflections whose intensities were 2
measured 2
x6 Undefined 2
4.2.7 CONDITIOns CONDITIOns 4.2.7
2
HKL Reflection ranges used in measuring intensities 2
a DIFF Type of diffractometer, 2
E = Enraf-Nonius 2
G = GE-XRD 2
H = Hilger Watts 4 circle 2
P = Picker 2
S = Nicolet(Syntex) 2
W = Philips PW1100 2
X = other 2
x1 hMIN Minimum value of h used 2
x2 hMAX Maximum value of h used 2
x3 kMIN Minimum value of k used 2
x4 kMAX Maximum value of k used 2
x5 lMIN Minimum value of l used 2
x6 lMAX Maximum value of l used 2
2
STD Details of standard reflection used for monitoring intensity 2
measurements. Use as many cards as necessary 2
2
x1 h | 2
x2 k | Miller index of a standard reflection 2
x3 l | 2
x4 AVINT Average intensity measured 2
x5 SDINT Standard deviation 2
x6 Undefined 2
2
ABS Absorption correction to intensities 2
2
a TYPE Type of correction made. Give details if necessary 2
in the COMMENTS:ABS section (4.2.14) 2
A = analytical 2
E = semi-empirical 2
G = Gaussian 2
M = Monte Carlo 2
N = no correction made 2
-1 2
x1 ABS Linear absorption coefficient (mm ) 2
x2 AMIN Minimum absorption correction applied 2
x3 AMAX Maximum absorption correction applied 2
x4-x6 Undefined 2
4.2.7 CONDITIOns CONDITIOns 4.2.7
2
FACE Used for defining the shape and size of the crystal.
x1 R perpendicular distance from an arbitrary
origin to a crystal face (mm)
x2 h |
x3 k | Miller indices of the face
x4 l |
x5 CHI or KAPPA | polar coordinates of the normal to the face.
x6 PHI |
Note give (hkl) or (CHI or KAPPA, PHI) but not both. One card is needed 1
per crystal face. Whichever fields are not being used should be set to 1
999999999 to ensure that the values are not inadvertently read as zero. 1
If FACE cards are given, 3 ORNT cards or an OUB1 and an OUB2 card must also be2
given. If CHI or KAPPA and PHI are given then OMEGA is assumed to be the same2
as that on the first ORNT card and THETA is assumed to be zero. 2
FARE This card gives the standard errors of the quantities given on the 2
FACE card using the corresponding fields 2
ORNT Used for defining the crystal orientation on the diffractometer.
a blank 2
or DIFF Type of diffractometer (code as for CID = 'HKL ') 2
DIFF on CID = 'HKL ' should be used in preference 2
to this field. 2
x1 h |Miller indices (not necessarily integral) of
x2 k |an arbitrary point in reciprocal space.
x3 l |
x4 OMEGA |Angular settings on diffractometer used
x5 CHI or KAPPA |corresponding to these Miller indices. Use
x6 PHI |the definition of OMEGA, CHI or KAPPA and
|PHI normal for the diffractometer specified or
|define them in COMMENTS:ANGL (Section 4.2.14) 2
At least 3 ORNT cards should be given to define the direction and sense
of the axes.
OUB1 Orientation Matrix of crystal on diffractometer 1
a blank 2
or DIFF Type of diffractometer (code as for CID = 'HKL ') 2
It is recommended to use DIFF on CID = 'HKL ' 2
instead of this field. 2
x1 UB11 | 1
x2 UB12 |Two consecutive cards OUB1, OUB2 used to 1
x3 UB13 |define the orientation of the crystal by an 1
x4 UB21 |orientation matrix UB. 1
x5 UB22 |Use the definition of UB normal for the 1
x6 UB23 |diffractometer specified or define it in a 1
|COMMENTS:OUB (section 4.2.14). 1
| 1
OUB2 x1 UB31 | 1
x2 UB32 | 1
x3 UB33 | 1
4.2.7 CONDITIOns CONDITIOns 4.2.7
EQIV Merging of equivalent reflections 2
2
a Undefined 2
x1 NINT Total number of measured reflections 2
x2 SINT Total number of symmetry independent reflections 2
x3 RINT Agreement index between equivalent reflections 2
x4-x6 Undefined 2
2
REFN Details of the final refinement 2
2
a REFF Form of structure factor used in refinement 2
F = structure factors 2
S = square of structure factors 2
I = intensities 2
x1 MAXS/E Maximum shift/error 2
x2 AVS/E Average shift/error 2
-3 2
x3 MAXDD Maximum difference density (eA for X-ray 2
diffraction) -3 2
x4 MINDD Minimum difference density (eA for X-ray 2
diffraction) 2
x5 K Where IMIN = K*SIGMA(I(obs)) and reflections with 2
I > IMIN contribute in the refinement 2
For default use 9999999999 2
x6 THRESH Where reflections with I > THRESH contribute in the 2
refinement. For default use 9999999999. Give 2
K or THRESH and set the other to default 2
2
STAT Statistics of refinement 2
2
a REFS Form of structure factors used in agreement indices 2
F = structure factors 2
S = square of structure factors 2
I = intensities 2
x1 R Conventional agreement index (all reflections) 2
x2 WR Weighted agreement index (all reflections) 2
x3 S Goodness of fit 2
x4 ROBS Conventional agreement index for reflections with 2
I(obs).gt.IMIN 2
x5 K Where IMIN = K*SIGMA(I(obs)) 2
x6 NUNOBS Number of unobserved reflections 2
2
VAR Number of variables used in refinement 2
2
a Undefined 2
x1 NREF Number of reflections used in refinement 2
x2 NVAR Total number of parameters refined 2
x3 NGVR Number of global parameters refined 2
x4 NCVR Number of atomic coordinates refined 2
x5 NIVR Number of isotropic atomic displacement parameters 2
refined 2
x6 NAVR Number of anisotropic atomic displacement parameters2
refined 2
EOS End of section. No data given on this card.
*****************************************
4.2.8 FORMULA (A1, 2A4, 6(A2, F8.4), 6X) FORMULA 4.2.8
*****************************************
Col. Format
1 A1 EOS * on the last card of the section
2-5 A4 CID Card Indentifier: FORL (or blank), CRYS, ANAL 2
or EOS 2
6-9 A4 DSK Data Set Key (see section 3.6(c))
10-11 A2 | 1st element name
12-19 F8.4 | Number of atoms of lst element present
20-21 A2 | same for 2nd element
22-29 F8.4 |
30-31 A2 | same for 3rd element
32-39 F8.4 |
40-41 A2 | same for 4th element
42-49 F8.4 |
50-51 A2 | same for 5th element
52-59 F8.4 |
60-61 A2 | same for 6th element
62-69 F8.4 |
70-75 6X undefined
Use as many cards as necessary.
CID Value of parameter
--- ------------------
FORL The unit cell defined in section 4.2.1 should contain Z of these 2
or blank formula units. The use of FORL instead of blank is recommended. 2
CRYS formula derived from crystal structure analysis (if different) 1
1
ANAL formula derived from chemical analysis. 1
1
EOS End of section. No data given on this card.
**********************************
4.2.9 REFERENCe (A1, 2A4, 1X, A65) REFERENCe 4.2.9
**********************************
This section contains bibliographic information and information about the
origin of the entry
Col. Format
1 A1 EOS * on the last card of the section
2-5 A4 CID Card Identifier: JRNL, AUTH, TITL, CAS, PDB, RFCD, 2
INOR, METL, PDF, HIST, RMRK or EOS 2
6-9 A4 DSK Data Set Key (see section 3.6(c))
10 1X
11-75 A65 DATA data whose contents depend on CID (see below)
CID Value of parameter
--- ------------------
JRNL Journal reference.
11-12 A2 last 2 digits of year of publication
13-18 A6 ASTM Journal Coden (given on cover of the journal
or available from Chem. Abstracts Source List)
19-22 A4 volume number
23-27 A5 first page
28-32 A5 last page
33-75 A43 journal name (free text)
AUTH Authors' names, surname first, one name per card, use as many
cards as necessary.
TITL Title of paper, use as many TITL cards as necessary.
CAS Chemical Abstracts Service registry number (A10). 1
1
PDB Protein Data Bank entry identification code (A4). 1
1
RFCD Cambridge File Refcode (A8). 1
1
INOR Inorganic Database entry (collection) number (A6). 1
1
METL Metal File entry number. 1
1
PDF Powder Diffraction file number. 1
2
HIST History of modifications made to the data given in the entry 2
11-18 A8 Date modification made in form YEAR MOnth DAy 2
e.g.19870615 2
19-75 A57 Details of modification e.g. programs used, by whom 2
performed, etc. free text 2
RMRK Comments. 1
1
EOS End of section. No data given on this card.
**************************
4.2.10 REMARK (A1, A74) REMARK 4.2.10
**************************
Col. Format
1 A1 EOS * on the last card of the section.
2-75 A74 Any messages may be written in this section.
The COMMENTS section (4.2.14) should be used for 2
text whenever possible since it provides a more 2
structured method of presenting remarks. 2
**********************************************************
4.2.11 BONDS (A1, 2A4, 1X, 2(A2,A6), I2, A1, 6F7.4, 4X) BONDS 4.2.11 1
********************************************************** 1
1
This section can be used to provide a listing of the bonds. 1
1
Col. Format 1
1
1 A1 EOS * on the last card of the section 1
2-5 A4 CID Card Identifier: BOND (or blank), or EOS 1
The use of BOND instead of blank is recommended. 2
6-9 A4 DSK Data Set Key (see section 3.6(c)) 1
10 1X 1
11-12 A2 AN1 Atom name of origin atom 1
13-18 A6 AI1 Identifier of origin atom 1
19-20 A2 AN2 Atom name of terminal atom 1
21-26 A6 AI2 Identifier of terminal atom 1
27-28 I2 BT Bond type 1 = single 1
2 = double 1
3 = triple 1
4 = quadruple 1
5 = aromatic 1
6 = ionic 1
7 = delocalized 1
8 = Van der Waals 1
9 = metal-ligand PI bond 1
0 = unidentified or other 1
29 A1 A/C A/C acyclic or cyclic bond 1
30-36 F7.4 LENG bond length 1
37-43 F7.4 ELENG error in bond length 1
44-50 F7.4 BX | 1
51-57 F7.4 BY |components of bond (x2 -x1, etc.) along cell axes 1
58-64 F7.4 BZ |unless otherwise specified 1
65-71 F7.4 BO Bond strength, bond valence, bond number or bond 1
order 1
72-75 4X Undefined 1
1
****************************************************************** 1
4.2.12 CONNECTIon (A1, 2A4, 2(A2, A6, A3, 3I2), 4F7.4, I2, I1, A1) 4.2.12 2
****************************************************************** 2
2
This section is used to define the connection table and may contain bonds 2
(BT.NE.10) or other interatomic distances (BT.EQ.10) 2
2
Col. Format 2
2
1 A1 EOS * on the last card of the section 2
2-5 A4 CID Card identifier: DIST, VECT or EOS 2
6-9 A4 DSK Data set key (see section 3.6(c)) 2
10-11 A2 AN1 |Atoms forming the connection 2
12-17 A6 AI1 | AN Atom name | as in ATOMS section 2
18-20 A3 ASYM1 | AI Atom identifier | section (4.2.4) 2
21-22 I2 XT1 | ASYM Identifier of the symmetry operator 2
23-24 I2 YT1 | applied to the atom (see SYMMETRY:SYOP 2
25-26 I2 ZT1 | section 4.2.3)) 2
27-28 A2 AN2 | XT,YT,ZT Integer lattice translations applied 2
29-34 A6 AI2 | after the application of the symmetry 2
35-37 A3 ASYM2 | operator. Given in units of the unit 2
38-39 I2 XT2 | cell vector 2
40-41 I2 YT2 | 2
42-43 I2 ZT2 | 2
2
44-50 F7.4 x1 | 2
51-57 F7.4 x2 | Parameters whose value depends on CID 2
58-64 F7.4 x3 | 2
65-71 F7.4 x4 | 2
72-73 I2 i1 | 2
74 I1 i2 | 2
75 A1 a1 | 2
2
CID Value of parameter 2
--- ------------------ 2
2
DIST Used for reporting bond lengths and distances 2
2
x1 LENG Bond length 2
x2 ELENG Error in bond length 2
x3 BO Bond order or bond strength 2
x4 Undefined 2
i1 BT Bond type (same as in the BOND section (4.2.11) 2
except that BT = 10 means that the distance is 2
not a bond) 2
i2 CT (Reserved for link or connection type) 2
a1 C/A Cyclic or acyclic flag 2
2
VECT Used for giving the bond vector 2
2
x1 BX |components of the bond vector referred to the 2
x2 BY | crystallographic unit cell 2
x3 BZ | 2
2
EOS End of section. No data given on this card 2
2
*************************************
4.2.13 CRYSTAL (A1, 2A4, 2A3, 6F10.0) CRYSTAL 4.2.13 2
************************************* 2
This section contains data on refinable crystal parameters 2
2
Col. Format Data 2
2
1 A1 EOS * on last card of section 2
2-5 A4 CID Card identifier: SCAL, EXTN, EXTE, ABSR, 2
TWIN or EOS 2
6-9 A4 DSK Data set key (see section 3.6(c)) 2
10-12 A3 a1 | 2
13-15 A3 a2 |Parameters whose value depends on the CID 2
16-25 F10.0 x1 | 2
26-35 F10.0 x2 | 2
36-45 F10.0 x3 | 2
46-55 F10.0 x4 | 2
56-65 F10.0 x5 | 2
66-75 F10.0 x6 | 2
2
CID Value of parameter 2
--- ------------------ 2
2
SCAL Scale factors 2
2
a1-a2 Undefined 2
x1 S Scale factor. S multiplies the |F(obs)| to put them on 2
the same scale as the |F(calc)|. Thus both |F(obs)|**2 2
and I(net) need to be multiplied by S**2 to put them on 2
the same scale as |F(calc)|**2 and I(calc) respectively. 2
If S=0 (or blank) S=1.0 is assumed 2
x2 ES Standard error in S 2
x3-x6 Undefined 2
2
EXTN Extinction parameters 2
2
a1 Extinction theory flag 2
BAC = Becker and Coppens. Acta Cryst. (1974). A30, 129- 2
153. Acta Cryst. (1975). A31, 417-425. 2
LAR = Larson Acta Cryst. (1967). 23, 664-665. 2
(any other code should be defined in the COMMENTS:EXTN 2
section (4.2.14)) 2
4.2.13 CRYSTAL CRYSTAL 4.2.13
2
For a1 = BAC 2
a2 Parameter specifier (defines the parameters x1-x6) 2
11 A1 Directionality of correction 2
I = Isotropic (1 parameter) 2
A = Anisotropic (6 parameters) 2
12 A1 Parameter type 2
L = Mosaic spread with Lorentzian distribution 2
G = Mosaic spread with Gaussian distribution 2
F = Mosaic spread with Fresnelian distribution 2
D = Domain size parameter 2
13 A1 Parameter sub-type 2
blank = no sub-type 2
For A in 11 with L, G or F in 12: 2
C = Coppens and Hamilton expression for aniso- 2
tropic mosaic contribution, Acta Cryst. (1970) 2
A26,71-83. 2
T = Thornley and Nelmes expression for anisotropic 2
mosaic contribution, Acta Cryst. (1974). A30, 2
748-757. 2
x1 X11 or X(isotropic) | 2 2
x2 X22 | Units of milliradians (or inverse) 2
x3 X33 | for mosaic distribution parameters 2
x4 X12 | 2 2
x5 X13 | Units of micrometres (or inverse) for 2
x6 X23 | for domain size paramters 2
2
For a1 = LAR 2
a2 undefined 2
x1 g g factor 2
x2 SIGMA(g) Standard error in g 2
x3-x6 undefined 2
2
EXTE Errors in corresponding extinction parameter 2
2
NOTE: In the general case, two EXTN and two EXTE cards will be needed, 2
one to specify the mosaic distribution description and the other 2
to specify the domain size parameters. 2
2
2
ABSR Gives information on the absolute structure (chirality or polarity) 2
2
a1 Undefined 2
a2 Undefined 2
x1 X Absolute-Structure parameter. 2
x2 SIGX Error in X. 2
x3-x6 Undefined 2
4.2.13 CRYSTAL CRYSTAL 4.2.13
2
TWIN Gives information on the volume fractions of twin components 2
Use as many TWIN cards as necessary 2
2
a1 ATWIN User defined twin identifier. This must be the same as 2
that used to specify the corresponding twin symmetry 2
operation in the SYMMETRY:TWIN (section 4.2.3) 2
a2 Undefined 2
x1 TVOL Volume fraction of the twin. The sum of all volume 2
fractions should be 1.0 2
x2 ETVOL Error in TVOL 2
x3-x6 Undefined 2
2
2
EOS End of section. No data given on this card. 2
********************************** 2
4.2.14 COMMENTS (A1, 2A4, 1X, A65) COMMENTS 4.2.14 2
********************************** 2
2
Section for strutured comments and text. 2
2
Col. Format Data 2
1 A1 EOS * on last card of section 2
2-5 A4 CID Card identifier: ABST,INTR,EXPT,DESC,DISC,UPAC, 2
NAME,SRCE,PREP,FORM,PHAS,ANGL,ABS, 2
OUB,EXTN,SSOL,SCAT,WGHT,HYDR,PROG,ORIG, 2
SYOP,SPOS,DISO,EOS 2
6-9 A4 DSK Data set key (see section 3.6(c)) 2
10 1X 2
11-75 A65 TEXT Text according to CID below. 2
Use free format text to give appropriate 2
information. 2
If necessary, use several cards with the same 2
CID. 2
2
CID Value of parameter 2
--- ------------------ 2
ABST Text of abstract of paper 2
2
INTR Text of introduction to paper 2
2
EXPT Text of description of experimental method 2
2
DESC Text describing the structure or crystal properties etc. 2
2
DISC Text discussing the results of the experiment 2
2
UPAC IUPAC name, use as many cards as necessary 2
2
NAME Other chemical name (e.g. synonym or trivial name) 2
2
SRCE Description of the source of the material 2
2
PREP Description of the preparation of the material 2
2
FORM Chemical formula in free format (see also FORMULA Section (4.2.8) 2
2
PHAS Information about the solid state phase 2
2
ANGL Definition of angles used in the diffractometer (see HKL:ANGL section 2
(4.2.6) and CONDITIOns:ORNT section (4.2.7)) 2
2
ABS Details of absorption correction (see CONDITIOns:ABS section (4.2.7)) 2
4.2.14 COMMENTS COMMENTS 4.2.14 2
2
OUB Definition of orientation matrix (see CONDITIOns:OUB1 and OUB2 2
section (4.2.7)) 2
2
EXTN Details of extinction correction (see CRYSTAL:EXTN section (4.2.13)) 2
2
SSOL Method used for structure solution 2
2
SCAT Source of atomic scattering functions (form factors) 2
WGHT Description of the weighting scheme used in refinement 2
2
HYDR Treatment of hydrogen atoms in refinement 2
2
PROG List of programs used. Give each program on a different card 2
2
ORIG Choice of origin of unit cell (should agree with SYMMETRY (4.2.3) and 2
SG NAME (4.2.2) sections) 2
2
SYOP Algorithm used for generating symmetry operators (see SYMMETRY:SYOP 2
section (4.2.3)) 2
2
SPOS Algorithm used for generating special positions (see SYMMETRY:SPOS 2
section (4.2.3)) 2
2
DISO Description of disorder 2
2
EOS End of section. No data given on this card. 2
-------------------------------------------------------------------------------
*******************************************************************************
4.3 SECTIONS GIVING BASIC DATA IN COMPACT FORM 4.3
*******************************************************************************
-------------------------------------------------------------------------------
***********************************************************************
4.3.1 ATOM COOrdinates (A1, A2, A3, A4, 3F8.5, 2F6.4, 3F6.5, 2F5.4, 1X)
***********************************************************************
This contains atomic coordinates in a compact form. See ATOMS section
(4.2.4) for detailed definitions.
Col. Format
1 A1 EOS * on the last card of the section
2-3 A2 AN Atom name
4-6 A3 AI Atom identifier (any legal characters)
In other sections (e.g. ATOMS (4.2.4) and BONDS 2
(4.2.11) AI is given the format A6. The ATOM COO 2
section should only be used if AI consists of no 2
more than 3 characters. In this case, the right 2
hand three characters in the A6 format should be 2
blank 2
7-10 A4 AT Atom type (to identify form factors)
11-18 F8.5 x |
19-26 F8.5 y |Atomic coordinates in fractions of unit cell.
27-34 F8.5 z |
35-40 F6.4 U Isotropic (or equivalent isotropic) atomic
displacement parameter
2 2
T = exp(-8(PI) U (sin(THETA)/LAMBDA) )
41-46 F6.4 OCC Occupation number
47-52 F6.5 SIGMA(x) | Standard errors in x, y, z, U and OCC.
53-58 F6.5 SIGMA(y) |
59-64 F6.5 SIGMA(z) | N.B. If these are written as integers (I6 or
| I5), they will be read as errors in the 5th
65-69 F5.4 SIGMA(U) | (or 4th) decimal place
70-74 F5.4 SIGMA(OCC) |
75 1X undefined
********************************************************************
4.3.2 HKL PACK (A1, 3I3, F8.2, F6.2, A1, 2(1X, 3I3, F8.2, F6.2, A1)) 4.3.2
********************************************************************
A compact form listing 3 structure factors per card.
Col. Format
1 A1 EOS * on the last card of the section
2-4 I3 h |
5-7 I3 k |Miller indices
8-10 I3 l |
11-18 F8.2 |F(obs)| Observed structure factor for the first
reflection
19-24 F6.2 SIGMA(|F(obs)|)Error in |F(obs)|
25 A1 a Flag (see HKL (Section 4.2.6) for
definition)
26 1X
27-29 I3 h |
30-32 I3 k |
33-35 I3 l | as above for second reflection
36-43 F8.2 |F(obs)| |
44-49 F6.2 SIGMA(|F(obs)|)|
50 A1 a |
51 1X
52-54 I3 h |
55-57 I3 k |
58-60 I3 l | as above for third reflection
61-68 F8.2 |F(obs)| |
69-74 F6.2 SIGMA(|F(obs)|)|
75 A1 a |
A problem arises when the number of structure factors is not divisible by 3 1
since the last card will contain one or two reflections with hkl blank. 1
This might be read on some machines as (hkl) = (000) resulting in data 1
for the (000) reflection being overwritten. In this case h k and l 1
should be given the default values of 999. Alternatively any unused 1
parts of the card may be filled with 9's. 1
-------------------------------------------------------------------------------
*******************************************************************************
4.4 SECTIONS OF INTEREST TO MACROMOLECULAR CRYSTALLOGRAPHERS 4.4
*******************************************************************************
-------------------------------------------------------------------------------
******************************************************************************
4.4.1 ATOM MACromolecule (A6, I5, 1X, A2, 3A1, A3, 1X, A1, I4, A1, 3X, 3F8.3,
2F6.2, 1X, I3, A4, 1X)
******************************************************************************
This section is designed for macromolelcular structures and is compatible
with the format used in the Protein Data Bank. For further details see
"Protein Data Bank Atomic Coordinate and Bibliographic Entry Format
Description, January 1985" Dept. of Chemistry, Brookhaven National 2
Laboratory, Upton, N.Y., 11973, U.S.A.
Note that atomic coordinates are expressed in rectangular cartesian
coordinates in Angstrom units. The transformation matrix is given in
the ORTHOGONal section (4.4.2).
Since this format is compatible with the Protein Data Bank format the
first six columns are used for the CID. The end of section is indicated
using "*EOS " as a CID.
Col. Format Data
1-6 A6 CID ATOM, SIGATM, HETATM, TER or *EOS.
ATOM records are used for atoms in the
principal structural units.
SIGATM records contain standard errors in
coordinates.
HETATM records are identical to ATOM records
but are used for water and atoms in other HET
groups.
TER records use only columns 1-27 and occur
after the terminal atom of each chain when the
chemically-identified terminal residue occurs
as the last residue in the coordinate list.
*EOS is the end of section and contains no
data.
7-11 I5 Atom serial number
12 1X
13-14 A2 AN Atom name (element symbol, right justified)
15 A1 Remoteness indicator
16 A1 Branch designator
17 A1 Alternative location indicator
18-20 A3 Residue name
or
(15-20 A6 AI Atom identifier, any legal characters)
4.4.1 ATOM MACromolecule ATOM MACromolecule 4.4.1
21 1X
22 A1 Chain identifier
23-26 I4 Residue sequence No.
27 A1 Code for insertion of Residues
28-30 3X
31-38 F8.3 X |Atomic coordinates in ANGSTROM UNITS (or their
39-46 F8.3 Y |standard errors (ANGSTROM UNITS) if CID =
47-54 F8.3 Z |"SIGATM")
55-60 F6.2 OCC Occupancy (standard error if CID = "SIGATM").
Normally 1.0.
61-66 F6.2 B Isotropic atomic displacement factor (standard error
if CID = "SIGATM"). If anisotropic atomic 2
displacement factors are given in an ANIS MAC 2
section (4.4.4) this field may contain U(eq) 2
67 1X
68-70 I3 Footnote number
71-74 A4 AT Atom type (to identify scattering factors).
See ATOMS (Section 4.2.4).
75 1X Undefined
************************************************************************
4.4.2 ORTHOGONal Transformation (A5, I1, 1X, I3, 3F10.5, 5X, F10.5, 20X) 4.4.2
************************************************************************
This section is compatible with the Protein Data Bank format and is used in
conjunction with the ATOM MAC section.
Col. Format Card Format (see below for explanation)
1-5 A5 CID SCALE, ORGIX, MTRIX, TVECT or *EOS (*EOS = end
of section card containing no data)
6 I1 LNUM line number of matrix (1, 2 or 3 below)
(SCALE, ORGIX and MTRIX cards only)
7 1X
8-10 I3 SNUM Symmetry transformation number (MTRIX and
TVECT cards only)
11-20 F10.5 Mi1 |
21-30 F10.5 Mi2 |One row of matrix elements (i = LNUM)
31-40 F10.5 Mi3 |
41-45 5X
46-55 F10.5 Ti Translation element of matrix (i = LNUM)
56-58 3X Undefined.
59-60 I2 IG Coordinate flag (see below)
61-75 15X Undefined
This section contains the matrices used in transforming the orthogonal
coordinates given in the ATOM MAC section. If atomic coordinates are
given in ATOM MAC at least three SCALE cards should be included to give
the matrix that transforms orthogonal coordinates to crystal
coordinates.
Each matrix requires 3 cards where the matrix is stored in columns 11-55
as follows:
LNUM = 1, X' = M11*X + M12*Y + M13*Z + T1
LNUM = 2, Y' = M21*X + M22*Y + M23*Z + T2
LNUM = 3, Z' = M31*X + M32*Y + M33*Z + T3
For SCALE cards M = S and T = U
For ORGIX cards M = O and T = T
For MTRIX cards M = M and T = V, IG=1 if the coordinates of the atoms
related by the operations M/V are
given in the file
=0 otherwise
For TVECT cards M1i = Wi
4.4.2 ORTHOGONal transformation ORTHOGONal transformation 4.4.2
The fractional (crystallographic) coordinates x are related to the
orthogonal coordinates X given in the ATOM MAC section by x = S*X + U.
The coordinates originally submitted to the Protein Data Bank (X2) are
given by X2 = O*X + T
When the asymmetric unit contains atoms related by non-crystallographic
symmetry these can be generated by X'=M*X+V. In a polymeric structure
the full structure can be generated by applying succesively the vector
given on the TVECT card to the coordinates in ATOM MAC X' = X + W. Each
MTRIX and TVECT card must contain a serial number in SNUM, each operation
having a different value of SNUM.
The TVECT card should be blank in columns 46-55.
For further details of the use of these matrices see Appx A of the
"Protein Data Bank. Atomic Coordinate and Bibliographic Entry Format
Description, January 1985". 2
******************************************************************
4.4.3 HKL PROTein (A1, 3I4, A4, 2(F6.0, F4.0), 3I3, 4F5.0, I6, I3) 4.4.3
******************************************************************
This section is designed for protein structure factors.
Col. Format
1 A1 EOS * on the last card of the section
2-5 I4 h |
6-9 I4 k |Miller indices
10-13 I4 l |
14-17 A4 DSK Data set key (see section 3.6(c))
18-23 F6.0 |F(obs)| Observed structure factor
24-27 F4.0 SIGMA(F(obs)) Standard error in F(obs)
28-33 F6.0 DELTA |F(obs) |-|F(obs) ___|
hkl hkl
34-37 F4.0 SIGMA(DELTA) Standard error in DELTA
38-40 I3 ALPHA(p) most probable phase of native protein
41-43 I3 ALPHA(b) best (i.e. centroid) phase of native protein
44-46 I3 m Figure of merit (100)
47-51 F5.0 A | Coefficients in the expression
52-56 F5.0 B | logP(ALPHA) = Acos(ALPHA) + Bsin(ALPHA) +
57-61 F5.0 C | Ccos2(ALPHA) + Dsin2(ALPHA) scaled by scale
62-66 F5.0 D | factor given in the CONDITIOns section.
67-72 I6 |F(calc)| | calculated structure factor and phase (in
73-75 I3 ALPHA(calc) | degrees) for native protein.
By a suitable choice of the scale given in the CRYSTAL:SCAL section(4.2.13), 2
these numbers can be given as integers if space is short.
Fields given as Fn.0 should normally contain only integers.
They would not include the decimal point and could be read
as if they were written as In. Correctly scaled values are
calculated by multiplying the integers given in these fields by the scale
factor given in CRYSTAL:SCAL Section (4.2.13).
************************************************************** 2
4.4.4 ANIS MACromolecule (A6, I5, 1X, A2, 3A1, A3, 1X, A1, I4, 2
A1, 1X, 6F7.4, 5X) 4.4.4 2
************************************************************** 2
2
This section is used for reporting anisotropic atomic displacement factors 2
2
col. format data 2
2
1- 6 A6 CID ANISOU for anisotropic atomic dispaclement factors 2
SIGUIJ for standard errors in ANISOU 2
*EOS for end of section (last card) 2
7-27 Same as ATOM MAC section (4.4.1) 2
28 1X 2
29-35 I7 U11 | 2 2
36-42 I7 U22 |Anisotropic atomic displacement factors 10**4 in A 2
43-49 I7 U33 | in the rectangular coordinate system used for 2
50-56 I7 U12 | the atomic coordinates. 2
57-63 I7 U13 | (see ATOMS:UIJ section (4.2.4) for definition) 2
64-70 I7 U23 | 2
71-75 5X Undefined 2
2
**************************************** 2
4.4.5 CONN MACromolecule (A6, 11I5, 14X) CONN MACromolecule 4.4.5 2
**************************************** 2
2
Gives atom connectivities for macromolecules 2
2
Col. format data 2
2
1- 6 A6 CID CONECT or *EOS (for last card in the section) 2
7-11 I5 Serial number of central atom (section 4.4.1 cols 7-11) 2
12-31 4I5 Serial numbers of covalently bonded atoms 2
32-41 2I5 Serial numbers of acceptor hydrogen bonded atoms 2
42-46 I5 Serial number of salt bridged atom with excess negative 2
charge 2
47-56 2I5 Serial number of donor hydrogen bonded atoms 2
57-61 I5 Serial number of salt bridged atom with excess positive 2
charge 2
62-75 14X Undefined
-------------------------------------------------------------------------------
*******************************************************************************
4.10 SECTIONS DEFINED IN EARLIER VERSIONS AND NOW SUPERSEDED. 4.10
*******************************************************************************
-------------------------------------------------------------------------------
These sections are obsolete and should NOT be used in preparing new files.
They are included here only to permit the reading of files
produced using the earlier standards.
*************************************************** 1
4.10.1 SPACE GRoup (3A1, 2X, A4, 2X, A11, 3A4, 41X) 1
*************************************************** 1
(Superseded by SG NAME (section 4.2.2))
Col. Format
1 A1 EOS * since this section should contain only 1
card there will always be an asterisk in
column 1.
2 A1 LT Lattice type P, A, B, C, F, I or H. Normally
the first character of the Hermann-Mauguin
space group symbol but for rhombohedral space
groups use P for the rhombohedral setting, H
for the hexagonal setting. Any program
reading the file should generate the lattice
translation operators from this symbol.
3 A1 CC Center Code, C = center of symmetry at the
origin (A, N or other symbol = no center at
origin). If C is specified, any program
reading the file should automatically generate
additional symmetry operators by inverting the
operators given in SYMMETRY (Section 4.2.3)
through the origin e.g. if x,-y,1/2+z is
given, -x,y,-1/2-z should be generated by the
program.
4-5 2X
6-9 A4 DSK Data Set Key (see section 3.6(c))
10-11 2X
12-22 A11 SG Hermann-Mauguin space group symbol for the
setting actually used (see section 4.2.2 but
note that for rhombohedral space groups
LT = 'P' implies rhombohedral setting, LT = 'H'
implies hexagonal setting)
23-26 A4 X0 Origin shift in the form 1/8 -3/8 1/4 etc.
27-30 A4 Y0 (4 characters per axis, right justified).
3l-34 A4 Z0 This describes a vector from the origin given
in the standard (International Tables) setting
to the origin of the cell used in the
description of the structure. The axis system
in which the vector is given is that defined
in the field SG above.
35-75 41X Undefined.
********************************************************* 1
4.10.2 ATOM (A1, 2A4, A2, A3, 6F8.5, I4, A1, A4, 4X) ATOM 4.10.2 1
********************************************************* 1
(Superseded by ATOMS (section 4.2.4)). See ATOMS for detailed
definitions.
Col. Format
1 A1 EOS * on the last card of section.
2-5 A4 CID Card Identifier = ATCO, ATCE, UIJ, BETA, BIJ,
UIJE, BETE, BIJE or EOS
(See Section 4.2.4)
6-9 A4 DSK Data Set Key
10-12 A2 AN atom name
12-14 A3 AI atom identifier, (any legal characters).
15-22 F8.5 x1 |
23-30 F8.5 x2 |
31-38 F8.5 x3 |
39-46 F8.5 x4 |Parameters whose value depends on CID (see
47-54 F8.5 x5 |section 4.2.4)
55-62 F8.5 x6 |
63-66 I4 i1 |
67 A1 a1 |
68-71 A4 a2 |
72-75 4X undefined
*********************** 2
4.10.3 CONDITIOns:blank CONDITIOns:blank 2
*********************** 2
CID Value of parameter (superseded by various other CID's and sections) 2
--- ------------------
blank a N = neutron diffraction, E = electron diffraction, X (or
blank) = normal X-ray diffraction, S = Synchrotron radiation.
x1 LAMBDA Wavelength (Angstrom Units)
x2 T Temperature (K)
x3 SCALE Scale factor. True F = SCALE*F given in HKL
sections (Sections 4.2.6, 4.3.2, or 4.4.3)
If this field is blank a value of 1.0 is
assumed
-1
x4 ABS linear absorption coefficient (mm )
-3
x5 DM Observed density (mg.mm )
-3
x6 DC Calculated density (mg.mm )
************************ 2
4.10.4 FORM FACtor:blank FORM FACtor:blank 4.10.4 2
************************ 2
CID Values of Parameters (Superseded by FORM FACtor:TABL) 2
--- -------------------- 2
blank Table of atomic scattering factors
x1 sin(THETA)/(LAMBDA)| one card needed for each value of 1
x2 f | sin(THETA)/(LAMBDA) for each type of 1
x3 f" | atom as specified by AN and/or AT 1
x4 f' | Note that f' may be included in x2 (in 1
| which case x4 = 0.0) or it may be 1
| given in x4 ( in which case it should 1
| not be included in x2) 1
-------------------------------------------------------------------------------
*******************************************************************************
5. Appendix I Example of an SCFS-87 file Appendix I 5
*******************************************************************************
-------------------------------------------------------------------------------
TITLE
* Trimercury bisniobiumpentafluoridesulfate HG3NBFS
REFERENCE
RMRK Submittted for publication to
JRNL INOCA
TITL The Preparation and crystal structures of Hg3 (Nb F5)2 S O4,
TITL Hg3 (Ta F5)2 S O4 and Hg4 (Ta2 F11)2
AUTH BROWN I.D.
AUTH GILLESPIE R.J.
AUTH MORGAN K.R.
AUTH SAWYER J.F.
AUTH SCHMIDT K.J.
AUTH TUN Z.
AUTH UMMAT P.K.
AUTH VEKRIS J.E.
*EOS
COMMENTS
DESC The compound contains Hg3(2+) ions that are linear (they lie on
DESC a two fold axis. The anion consists of two NbF5 groups linked
DESC by Nb-O bonds to an S O4 ion which also lies on a two-fold axis.
DESC There is a strong Hg-O bond colinear with the Hg3 ion that
DESC connects to the terminal O of the sulfate group.
*EOS
CELL DIMENSION A B C ALPHA BETA GAMMA Z
CELL 18.0580 15.7160 9.1710 90.0000 90.0000 90.0000 1.
ERRS 0.0100 0.0100 0.0100 0.0000 0.0000 0.0000
VOL 2600. 2. 5.485
*EOS
SG NAME
HERM F D D 2
HALL F 2 -2D
LATT NP
*EOS
HKL H K L F(OBS) SIGMA F(CALC)
CALC 0 0 -4 1789.300 7.100 1740.500
CALC 0 0 4 1774.500 7.100 1715.200
CALC 0 0 8 777.400 12.000 752.600
CALC 0 2 -6B 61.300 21.200 74.000
*EOS
5 Appendix Appendix 5
SYMMETRY
SYOP 1 0 0 0.0000000 0 1 0 0.0000000 0 0 1 0.0000000 1
SYOP -1 0 0 0.0000000 0-1 0 0.0000000 0 0 1 0.0000000 2
SYOP -1 0 0 0.2500000 0 1 0 0.2500000 0 0 1 0.2500000 3
SYOP 1 0 0 0.7500000 0-1 0 0.7500000 0 0 1 0.2500000 4
SYOP 1 0 0 0.0000000 0 1 0 0.5000000 0 0 1 0.5000000 5
SYOP -1 0 0 0.0000000 0-1 0 0.5000000 0 0 1 0.5000000 6
SYOP -1 0 0 0.2500000 0 1 0 0.7500000 0 0 1 0.7500000 7
SYOP 1 0 0 0.7500000 0-1 0 0.2500000 0 0 1 0.7500000 8
SYOP 1 0 0 0.5000000 0 1 0 0.0000000 0 0 1 0.5000000 9
SYOP -1 0 0 0.5000000 0-1 0 0.0000000 0 0 1 0.5000000 10
SYOP -1 0 0 0.7500000 0 1 0 0.2500000 0 0 1 0.7500000 11
SYOP 1 0 0 0.2500000 0-1 0 0.7500000 0 0 1 0.7500000 12
SYOP 1 0 0 0.5000000 0 1 0 0.5000000 0 0 1 0.0000000 13
SYOP -1 0 0 0.5000000 0-1 0 0.5000000 0 0 1 0.0000000 14
SYOP -1 0 0 0.7500000 0 1 0 0.7500000 0 0 1 0.2500000 15
SYOP 1 0 0 0.2500000 0-1 0 0.2500000 0 0 1 0.2500000 16
SPOS 1 0 0 0.0000000 0 1 0 0.0000000 0 0 1 0.0000000 116
SPOS 0 0 0 0.0000000 0 0 0 0.0000000 0 0 1 0.0000000 2 8
*EOS
ATOMS X Y Z U(EQ) OCC VAL WYCK AT TF
ATCO HG1 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 8A 1
ATCE HG1 2
UIJ HG1 0.032 0.033 0.034 -0.006 0.0 0.0
ATCO HG2 0.09930 0.11460 0.96730 0.00000 1.00000 2.00000 16B 1
ATCE HG2 0.00010 0.00010 0.00010 1
UIJ HG2 0.035 0.033 0.036 -0.006 -0.003 0.003
ATCO NB 0.19270 0.44080 0.74360 0.00000 1.00000 5.00000 16B 1
ATCE NB 0.00010 0.00010 0.00020 1
UIJ NB 0.031 0.026 0.028 0.001 0.002 0.003
ATCO S 0.25000 0.25000 0.85360 0.00000 1.00000 6.00000 8A 1
ATCE S 0.00000 0.00000 0.00050 2
UIJ S 0.030 0.025 0.029 -0.003 0.0 0.0
ATCO F 1 0.18080 0.55750 0.72750 0.00000 1.00000-1.00000 16B 1
ATCE F 1 0.00040 0.00040 0.00150 1
UIJ F 1 0.058 0.027 0.061 -0.003 -0.001 0.006
ATCO F 2 0.19600 0.42710 0.54390 0.00000 1.00000-1.00000 16B 1
ATCE F 2 0.00050 0.00060 0.00100 1
UIJ F 2 0.061 0.063 0.039 0.006 0.004 0.009
ATCO F 3 0.18810 0.43800 0.94860 0.00000 1.00000-1.00000 16B 1
ATCE F 3 0.00060 0.00070 0.00100 1
UIJ F 3 0.063 0.058 0.037 0.003 0.004 -0.006
ATCO F 4 0.09050 0.42330 0.73660 0.00000 1.00000-1.00000 16B 1
ATCE F 4 0.00040 0.00080 0.00200 1
UIJ F 4 0.039 0.054 0.057 -0.002 0.011 0.011
ATCO F 5 0.29640 0.45700 0.75360 0.00000 1.00000-1.00000 16B 1
ATCE F 5 0.00040 0.00060 0.00100 1
UIJ F 5 0.029 0.048 0.071 0.007 -0.013 0.007
ATCO O 1 0.21350 0.31180 0.75460 0.00000 1.00000-2.00000 16B 1
ATCE O 1 0.00060 0.00060 0.00100 1
UIJ O 1 0.043 0.018 0.049 0.004 -0.012 0.004
ATCO O 2 0.19550 0.20770 0.94460 0.00000 1.00000-2.00000 16B 1
ATCE O 2 0.00050 0.00060 0.00100 1
UIJ O 2 0.034 0.032 0.033 -0.009 0.004 -0.003
*EOS
5 Appendix Appendix 5
CONNECTION
DIST HG1 1 0 0 0HG2 1 0 0-1 2.559 0.001 1
VECT HG1 1 0 0 0HG2 1 0 0-1 0.0993 0.1146-0.0327
DIST HG1 1 0 0 0HG2 2 0 0-1 2.559 0.001 1
VECT HG1 1 0 0 0HG2 2 0 0-1-0.0993-0.1146-0.0327
DIST NB 1 0 0 0F 1 1 0 0 0 1.845 0.011 1
VECT NB 1 0 0 0F 1 1 0 0 0-0.0199 0.1167-0.0161
DIST NB 1 0 0 0F 2 1 0 0 0 1.858 0.014 1
VECT NB 1 0 0 0F 2 1 0 0 0 0.0033-0.0137-0.1997
DIST NB 1 0 0 0F 3 1 0 0 0 1.880 0.015 1
VECT NB 1 0 0 0F 3 1 0 0 0-0.0046-0.0228 0.2050
DIST NB 1 0 0 0F 4 1 0 0 0 1.854 0.011 1
VECT NB 1 0 0 0F 4 1 0 0 0-0.1022-0.0178-0.0070
DIST NB 1 0 0 0F 5 1 0 0 0 1.887 0.011 1
VECT NB 1 0 0 0F 5 1 0 0 0 0.1037 0.0162 0.0100
DIST NB 1 0 0 0O 1 1 0 0 0 2.070 0.013 1
VECT NB 1 0 0 0O 1 1 0 0 0 0.0208-0.1290 0.0110
DIST S 1 0 0 0O 1 1 0 0 0 1.479 0.015 1
VECT S 1 0 0 0O 1 1 0 0 0-0.0365 0.0618-0.0990
DIST S 1 0 0 0O 2 1 0 0 0 1.454 0.014 1
VECT S 1 0 0 0O 2 1 0 0 0 0.0365-0.0618-0.0990
DIST HG2 1 0 0 0F 1 5 0-1 0 2.9438 0.0147 1
VECT HG2 1 0 0 0F 1 5 0-1 0 0.0815-0.0571 0.2602
DIST HG2 1 0 0 0F 1 4-1 0 0 3.2812 0.0164 1
VECT HG2 1 0 0 0F 1 4-1 0 0-0.1685 0.0779 0.0102
DIST HG2 1 0 0 0F 2 7 0-1 0 3.2566 0.0162 1
VECT HG2 1 0 0 0F 2 7 0-1 0-0.0453 0.0625 0.3266
DIST HG2 1 0 0 0F 3 7 0-1-1 2.8034 0.0140 1
VECT HG2 1 0 0 0F 3 7 0-1-1-0.0374 0.0734-0.2687
DIST HG2 1 0 0 0F 5 14 0 0 0 2.9419 0.0147 1
VECT HG2 1 0 0 0F 5 14 0 0 0 0.1043-0.0716-0.2137
DIST HG2 1 0 0 0F 5 4-1 0 0 2.9807 0.0149 1
VECT HG2 1 0 0 0F 5 4-1 0 0-0.0529 0.1784 0.0363
DIST HG2 1 0 0 0O 2 1 0 0 0 2.2808 0.0114 1
VECT HG2 1 0 0 0O 2 1 0 0 0 0.0962 0.0931-0.0227
*EOS
5 Appendix Appendix 5
BONDS
BOND HG1 HG2 1 2.5591 0.0012 0.0993 0.1146-0.0327
BOND HG1 HG2 1 2.5591 0.0012-0.0993-0.1146-0.0327
*EOS
CONDITIONS
CELL X 0.71069 293 18 47 15
INT X 0.71069 293 0 1.15 2974
HKL S 0 23 -20 20 -11 11
STD 10 0 2 0.013
STD 0 10 2 0.012
ABS E 37.9 0.702 1.496
EQIV 2974 1515 0.036
REFN F 0.071 0.014 3.6 -6.1 9999999999 0
STAT F 0.048 0.045 0.048 0 0
VAR 1497 92 2 28 0 62
*EOS
FORMULA
FORL HG 3. NB 2. F 10. S 1. O 4.
*EOS
CRYSTAL
EXTN LAR .3E-04
EXTE LAR .1E-04
*EOS
COMMENTS
FORM HG3 (NB F5)2 S O4
ABS DIFABS correction
SSOL Patterson diagram and difference synthesis
SCAT SHELX76 (S,F,O)
SCAT International Tables for Xray crystallography Vol 4 (Hg,Nb)
WGHT k*(sigma(counting)+g*F**2)**(-1), k=0.9077, g=0.00035
PROG SHELX76
PROG DIFABS
SYOP Hall symbol interpretive routine from XTAL
SPOS Altermatt/Brown algorithm (to be published)
*EOS
END