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CRYSTALS manual
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Crystals Manual
Chapter 3: The Crystals Database
- 3.1: General List-control Directives - \DISK
- 3.2: Elimination of Old Versions of LISTS - \PURGE
- 3.3: LISTS in Current use
- 3.4: Printed Summary of Data lists
- 3.5: Element and Atom names
- 3.6: Foreign Program Links
- 3.2: Elimination of Old Versions of LISTS - \PURGE
It is a direct-access binary file. DO NOT try to print or edit it.
The data is organised in this file as lists, corresponding to the
external user-input lists. In modern terminology, these 'lists'
would be called 'objects' or 'data structures'. Each list groups
together related information, e.g. the cell parameters, the atoms,
the reflections etc.
While in general input of a list will
overwrite a previous version, for the atomic coordinate list (LIST 5,
see section 6.3) a
new version is added to the database. In the event that a refinement
goes wrong, the user can usually recover an earlier version of the
structure.
In the CRYSTALS system, most of the data required to refine a crystal structure must be input to the computer as ASCII, translated into an internal format and stored on a random access disk file. On the disk, different types of data are recorded separately, in what are called LISTS. Each list holds only one type of crystallographic information and is identified by a number called the 'list type number'.
Normally, each structure uses a separate disk file, which is preserved between different jobs and updated whenever a program generates some new data. This means that several different versions of a given list may be produced during the course of a structure analysis. In order that each list may be uniquely identified, every list has associated with it a second number, called the 'list serial number'. To specify unambiguously a list that is stored in the database, it is necessary to know both the relevant list type number and the list serial number.
In most cases, however, the version of a given list that is required is the latest list of that type to be created. Accordingly, an index called the 'current list index' is maintained, which contains an entry for the latest version of each list. When a program requires information about the current version of a list, it accesses the current list index.
As well as an index of the current version of each list, a second index is kept, called the 'file index'. For each disk file, this latter index contains the information for every list that is present in the database. This index is always checked when a list is written to the database, to ensure that its list type number and list serial number refer to only one list.
For a user, the major advantage of splitting the input data into logical units in the database is that, for any run, only those lists which need to be changed have to be re-input to the database. New versions of each list that are generated by programs are automatically output to the database so that, provided the database file is not destroyed or erased, it is probable that each run will contain only control commands. For example, during a structure factor least squares calculation a new set of Fcalcs and a new normal matrix will be generated and stored in the database ready for further calculations.
Old versions of a list may be reused, provided that they have not been overwritten or deleted, by finding the relevant entry in the file index and copying it into the current list index.
The database contains two indices which control access to it.
This index contains the serial numbers of each list to be used in calculations. This index is updated whenever a list is written to database.
This is an index of all the lists contained in the database. When a
new list is added to the database, its internal address is added to this
index, and also inserted into the current disk index. It is possible to
copy address from this index to the current disk index, thus changing
the currently active version of a list.
[Top] [Index] Manuals generated on Wednesday 8 November 2006
3.1: General List-control Directives - \DISK
The list control table can be marked and used in various ways with this command.
\DISK PRINT INDEX= PUNCH= LIST= MARKERROR LIST= SERIAL= RELATIVE= ACTION= RETAIN LIST= SERIAL= RELATIVE= ACTION= DELETE LIST= SERIAL= RELATIVE= ACTION= RESET LIST= SERIAL= RELATIVE= USAGE LIST= SERIAL= RELATIVE= FLAG= EXTEND RECORDS= FREE= TRIES= SIZE= CHECK END
For example:
\DISK \ Print the current list index PRINT INDEX=CURRENT \ Print the index containing all the lists stored \ on the disk PRINT INDEX=DISK \ Reset LIST 5 (the model parameters) to the one with serial number 4 RESET 5 4 \ Reset LIST 10 (Fourier peaks) to the 'current serial number - 1' RESET 10 0 -1 \ Retain LIST 5 with serial number 6 when the disk \ is purged RETAIN 5 6 \ Delete current LIST 11 (normal/inverted least squares matrix) DELETE 11 END
This is the command which initiates the routines to modify the list control table. The directives MARKERROR, DELETE, RETAIN, USAGE, and RESET all accept the parameters SERIAL and RELATIVE. The parameters SERIAL and RELATIVE should not both be changed from their default settings on the same directive.
All directives are executed immediately after they have been entered.
This directive causes one of the indexes to be printed.
CURRENT - default value
DISK
SUMMARY
If 'INDEX' is 'CURRENT', the current list index is
printed (i.e. the index containing the current version of each
list stored).
If 'INDEX' is 'DISK', the index containing information about all
the lists stored on the disk is printed.
If 'INDEX' is 'SUMMARY', a summary of the usage of the disk file is printed.
NO - default value
YES
Writes a machine readable summary of whatever is selected by INDEX to
the currently open PUNCH file.
This directive can either mark a specified type of list as an 'error list', or alternatively, such a mark can be removed from the list control table.
NO
YES - default value
If ACTION is NO , the entry in the list control table for the list type
specified is altered so that it is not marked as an 'error list'.
If ACTION is YES, the entry in the list control
table for the list type specified is altered so that it is marked as an
'error list'. If a program attempts to use such a list, an error is
reported, and the job terminated.
With this directive, certain old versions of specified lists can be retained when the disk file is PURGED (see 3.2).
NO
YES - default value
If 'ACTION' is 'YES', the list with the specified
type and serial number will be retained when the disk file is PURGED.
If 'ACTION' is 'NO' , the particular list will be deleted when the
disk file is PURGEd (see section 3.2).
With this directive certain lists can be deleted from the file index.
NO
YES - default value
If 'ACTION' is 'YES', the list with the specified
serial number will be marked to be deleted from the file when the
file is PURGED.
If ACTION is 'NO' , the specified list will not be marked as one to
be deleted when the disk file is PURGEd (see section 3.2).
OVERWRITE
READY
UPDATE - default value.
If only certain lists are unusable, use the DELETE directive in \DISK to mark defective LISTS for deletion, and then use \PURGE NEW to create a new disk file (by default new.dsc). Rename new.dsc to crfilev2.dsc to make CRYSTALS open it by default when it starts in that directory.
The following lists can always safely be deleted since CRYSTALS creates new ones automatically.
10 Fourier peaks (section 8.6).
11 Normal matrix (section 7.49).
20 Saved geometrical transformation matrices (section 9.6).
22 Constraints in internal format (section 7.49).
24 Least squares shift list (section 7.49).
26 Restraints in internal format (section 7.49).
33 SFLS command in internal format (section 7.42).
36 List dependency tracking (not documented).
See section 3.3 for all the list definitions.
Example 1
Imagine that the current versions of LIST 5 (the model parameters)
and LIST 29 (element properties) have beome corrupt.
We will also delete any recreatable lists.
\DISK
\ Check the index
CHECK
\ Delete current version of atomic params
DEL 5
\ Point index to the previous version
RESET 5 0 -1
\ Remove corrupt and safe-to-delete lists:
DEL 29
DEL 10
DEL 11
DEL 20
DEL 22
DEL 24
DEL 26
DEL 33
DEL 36
END
\ Open a new file save.dat on the 'PUNCH device'.
\ Release is equivalent to CLOSE followed by OPEN.
\RELEASE PUNCH SAVE.DAT
\ Output the important data lists:
\PUNCH 5
END
\PUNCH 12
END
\PUNCH 16
END
\ Write a new database called rescue.dsc with only the
\ current index of lists in it:
\PURGE RESCUE
\ Close CRYSTALS
\FINISH
At this point it would be useful on a stand-alone computer to
run a system utility (e.g. SCANDISK on a PC) to check the integrity of
the computers hard disk, since CRYSTALS rarely corrupts the disk itself.
One would then open a command prompt in the working folder and do this:
del crfilev2.dsc
ren rescue.dsc crfilev2.dsc
Now restart CRYSTALS in the same folder. Recover the important saved
data by typing:
\USE save.dat
[Top] [Index] Manuals generated on Wednesday 8 November 2006
3.2: Elimination of Old Versions of LISTS - \PURGE
\PURGE FILE= INITIALSIZE= LOG= LIST= END
This command deletes all but the current version of each list, and any lists explicitly marked to be deleted, except for lists marked to be retained, and then rewrites the disk file so that the space occupied by the old deleted lists is overwritten. This operation does not normally shorten the file physically (see parameter FILE below for a method of doing this) , but frees a lot of space that can be reused. The optional parameters 'FILE' and 'INITIALSIZE' (available in some implementations only), allow the user to create a new file with only the current version of each list in it. This file may be smaller than the original disk file.
OLD - default value
name - The root to be used form the new database - name.DSC
DATE - The root name is generated by CRYSTALS from the date and
time.
This parameter controls whether a new file is created. If the value specified is not OLD, a new file will be created containing only the current versions of each list, and any which are marked to be retained. The program automatically extends the file to the size required for all the lists to be retained. This new file has the extension .DSC, and may be used in future CRYSTALS tasks.
This parameter is used to specify an initial size for a new file. If a new file is not to be created, the value is ignored. The default value of zero causes the new file to have the smallest size necessary to contain all the copied lists.
OFF - default value
ON
If the value 'ON' is given for this parameter, the types and serial numbers of all lists deleted because they were old versions are listed. The types and serials of all lists not copied for other reasons, e.g. deleted lists, and lists which are marked as being updated, are always listed
[Top] [Index] Manuals generated on Wednesday 8 November 2006
3.3: LISTS in Current use
List Number Type of data
1 Cell parameters (section 4.2)
2 Unit cell symmetry (section 4.8)
3 Atomic scattering factors (section 4.11)
4 Weighting parameters (section 7.28)
5 The model parameters (section 6.3)
6 Reflection data (section 5.3)
7 Reflection data not used for refinement (section 5.4)
10 Peak coordinates from Fourier (section 8.6)
11 Least squares matrix (section 7.49)
12 Refinement directives (section 7.11)
13 Crystal and collection data (section 4.13)
14 Fourier directives (section 8.2)
16 General Restraints (section 7.17)
17 Special Restraints (section 7.24)
20* Transformation matrices saved by \GEOMETRY (section 9.6)
22* Refinement directives in internal format (section 7.49)
23 Structure factor control list (section 7.7)
24* Least squares shift list (section 7.49)
25 Twin component operators (section 10.0)
26* Constraints in internal format (section 7.49)
27 Diffractometer scales (section 5.12)
28 Reflection condition/filter list (section 7.39)
29 Contents of asymmetric unit and elemental properties (section 4.15)
30 General information (section 4.17)
31 Cell parameter E.S.D.'s (section 4.5)
33* Internal - Refinement control (last SFLS command, see 7.42)
36* Tracking interdependencies of parameters, normal matrix, weights etc.
40 Bond forming/breaking directives (section 6.13)
41* Bonds between atoms (section 6.12)
[Top] [Index] Manuals generated on Wednesday 8 November 2006
3.4: Printed Summary of Data lists
\SUMMARY OF= TYPE= LEVEL=
END
For example:
\ Detailed list of model parameters:
\SUMMARY OF=LIST TYPE=5 LEVEL=HIGH
END
\ Again, but less typing:
\SUM L 5 HI
END
\ Summary of reflection data:
\SUM L 6
END
This parameter determines the extent of the data summary.
LIST
EVERYTHING
If 'LIST' is specified, a summary of a specific list whose type is given by the 'TYPE' parameter is produced. If 'EVERYTHING' is specified, a summary of all current lists for which summaries are available is produced. If 'OF = EVERYTHING' is specified, the value of 'TYPE' is ignored.
This parameter indicates the
list type for which a summary is required. If a summary of this list
type is not available, a warning message will be printed.
LOW
MEDIUM
HIGH
This parameter has three values which indicate the level of detail
required in the data summary. The parameter is ignored unless the list
type is 5 or 10.
List Level Data printed ---- ----- ---- ------- 5 or 10 LOW Atom names 5 or 10 MEDIUM Atom names and positional parameters 5 or 10 HIGH All atomic and overall parameters
[Top] [Index] Manuals generated on Wednesday 8 November 2006
3.5: Element and Atom names
Elements are specified by a name, called the atom TYPE. The
'TYPE' is used to associate the refined atoms with atomic properties,
such as form factors, radii, etc. The TYPE must start with a letter,
and is not case sensitive.
REMEMBER that 'blank'
is used as a delimiter in CRYSTALS and so must
not appear in an atom TYPE. Elements in the form factor list (LIST 3 - see
section 4.11)
and the atomic properties (LIST 29 - section 4.15) are associated by
their TYPE with atoms in the parameter list (LIST 5). Numeric properties of the
elements are pre-prepared in the files SCATT, SCATCU, SCATMO and
PROPERTI(.dat) in the SCRIPT directory (Often CRYSTALS\SCRIPT). The
'elements' C', C", H' and H" are in these files with the properties of C and H.
You can define your own element names, but may not use +,- or *.
Individual atoms are specified by combining the TYPE with a SERIAL number. This is an integer in the range 1-9999. When combined with the TYPE, it must be enclosed in parentheses ().
e.g. C(2) CL(123)
Atoms specified as above correspond exactly to those in the refinable atom list (LIST 5). If a symmetry equivalent atom is required, up to 5 additional items are included inside the parentheses. The full specification of an atom is:
TYPE(SERIAL,S,L,Tx,Ty,Tz)
If the value of an item is its default, it may be omitted altogether, though its place must be marked by its associated comma. A series of trailing commas may also be omitted. For example:
C(99,-1,1,0,0,0) - an atom related by inversion at the origin
(assuming x,y,z is the first operator).
C(99,-1,1,,,0) - same atom as above, omitting defaults.
C(99,-1) - same atom as above, omitting
defaults and trailing commas.
For more detailed information, see Atomic and
Structural parameters (section 6.0)
[Top] [Index] Manuals generated on Wednesday 8 November 2006
3.6: Foreign Program Links
This command provides links to 'FOREIGN' programs, that is, programs which are not part of CRYSTALS, but which provide useful functions in providing a complete system. These programs often come from other laboratories, and are only distributed with the authors permission unless they are public domain. Where practical, we make no changes to the original code. We offer little or no support in connection with these programs, though usually they are in frequent use in Oxford. The linking routine prepares data files for the foreign program, and may initiate a subprocess to execute the rogram.
SNOOPI - A plotting program using Tektronix 4010 devices.
CAMERON - An interactive graohics program.
MULTAN - Prepares files for MULTAN 84.
SHELXS - Prepares files for SHELXS.
SIRxx - Prepares files for the SIR direct methods system
This keyword controls the mode of operation of the foreign program. It currently only applies to SHELXS and SIR.
NORMAL - DEFAULT, prepares a default data file with recommended
settings.
DIFFICULT - Prepares a file with non-default settings.
PATTERSON - Prepares a default Patterson calculation (SHELXS only).
SPECIAL - Prepares a full SHELX data file (SHELX only)
[Introduction To The System | Definitions And Conventions | The Crystals Database | Initial Data Input | Reflection Data Input | Atomic And Structural Parameters | Structure Factors And Least Squares | Fourier Routines | Analysis Of Results | Twinned Crystals | Matrix Calculations | Obsolete Commands ]
