CSD System Release Notes


April 1998 Version 5.15

Table Of Contents

  1. Introduction
  2. Database Content
  3. Software Expiry Date
  4. Documentation
  5. Graphics Quest3D
  6. Pluto
  7. Vista
  8. Gstat
  9. PreQuest
  10. Planned Changes


1. Introduction


The URL for the CCDC World Wide Web site is:

http://www.ccdc.cam.ac.uk

This site always includes details of any known problems and solutions relating to current releases of the CSD System.

(Please update any links and references to our original URL - http://csdvx2.ccdc.cam.ac.uk. This old address may cease to work in future, but http://www.ccdc.cam.ac.uk will always be updated).

Note that our domain name for e-mail has changed to ccdc.cam.ac.uk (instead of chemcrys.cam.ac.uk)

The e-mail address for User Support is now:

support@ccdc.cam.ac.uk


2. Database Content


The statistics for the three release databases are as follows:


Database Number of entries Last MDATE
Cambridge Master 181,309 980202 PDB Entries 7,157 980219 CSDS Citations 631 980209
Total 189,097
The CCDC distributes PDB data in two formats:

  • A CSD PDB ASER database which can be search using Quest and is located on the Unix and VMS release CD-ROMs.
  • A PDB CD-ROM containing 3D coordinates files for PDB entries.

The CSD PDB ASER database contains all 7157 entries released by Brookhaven up to and including 4 February 1998.

The PDB CD-ROM contains coordinate files for all entries released by Brookhaven up to and including 4 February 1998 that have been determined by diffraction experiments. NMR and theoretical modelling studies are not included on the PDB CD-ROM distributed by the CCDC with this release.

Coordinate files for NMR and theoretical models have been excluded to allow our distribution of PDB coordinates to fit onto one CD-ROM.

The entries excluded were:

  • 1116 NMR studies
  • 179 Theoretical models

A list of the pid codes of the structures excluded from this release of the CCDC PDB CD-ROM is located in the /doc/piddel.pid on the release CD-ROM.

The PDB CD-ROM thus contains 5862 coordinate files for PDB entries studied by diffraction.

As a consequence of these ommisions, coordinates of NMR and theoretical PDB entries will not be available to users accessing PDB coordinates from the CCDC PDB CD-ROM (either through the Quest-Rasmol link or through PDBGET). Users accessing PDB files from other sources should notice no difference, assuming their installation is complete.

Text, numeric and sequence searching of the CSD PDB ASER database are unaffected by these changes.


3. Software Expiry Date


The UNIX and VMS Packages expire at the end of December, 1998.

During December 1998, each time Quest is started under VMS, it will count down the number of days to expiry.

UNIX Quest always reports the number of days remaining.


4. Documentation


We have recently completed a major overhaul of the HTML documentation supplied with the CSD System.

The previous flat directory structure of the .html and associated graphics files distributed on the release CD-ROM (html/ on the Unix CD and [DBASE.RELEASE.DOC.HTML] on the VMS CD) has been replaced by a series sub-directories for different manuals or manual volumes, each with an associated images directory for graphics.

Three new HTML documents are also included for the first time. These are:

Volume 3, in particular, has been extensively updated since hardcopies of the Manuals were last printed. Appendices 2, 3, 4 & 5 are complete re-writes of the printed Manuals.

All of the new documents can be accessed by following links from the top level zdocmain.html file in the html directory.

Additionally, it is now possible to access all of the CSD System documentation available in .html format via our Website at:

http://www.ccdc.cam.ac.uk/support/csd_doc/zdocmain.html


5. Graphics Quest3D


Changes announced in the October 1997 Release

In the October 1997 release we announced our intention to make two changes to Quest3D.

Bug fixes

Bug fix: 'SAVE MOL2' is now better behaved for entries with suppressed atoms.

Bug fix: 'SAVE MOL2' crashed or gave garbage in the RESidue number field for entries with more than 160 'residues'. This has now been fixed

Bug fix: During the October 1997 changes to chemical class, a bug was introduced into the 'SAVE FBIB' code, which caused the last character of the journal name to be lost. This has now been fixed.

Bug fix: The 'FAST CONTINUE with NO-DIAGRAMS' facility now correctly turns off the graphical display.

Bug fix: The chemical class is now shown in the 1D Display.


6. Pluto


Several important enhancements to the Pluto program have been made for this release and a number of new menu buttons have been added.

New features

New feature: The HBOND button now calculates intra- and/or inter-molecular hydrogen bond D-H...A contacts on basis of default or user-defined geometrical criteria. This is dependent on H-atom coordinates being present.

New command: COL HBOND. Crystallographically-equivalent H-bonds or other non-bonded contacts are colour coded. This allows the path traced by a particular contact to be followed through a structure using EXP.

New experimental feature: GSET allows determination of graph sets for hydrogen-bonded networks up to second level on basis of contacts determined by HBOND. Currently under development and subject to certain limitations.

New command: COL MOTIF one may colour particular graph set motifs by typing COL MOTIF m for first level, or mn for second level (pattern involving H-bonds m and n).

New menu button: SLICE gives a packing slice through crystal in a given plane with several available control options.

New command: HNORM which re-normalises X-H distances, for X = C, N, O as QUEST command HNORM.

New command: HCAL to calculate hydrogen atom positions on the basis of intramolecular geometry.

New command: FDAT to provide output of current coordinates in FDAT format.

New command and menu button: STYLE to change linewidth, character size and plot step for circle drawing.

New command and menu button: TEXT to annotate plot for slides and publications.

New menu button: PLANE, which provides mean-plane view through (up to 16) selected atoms (command VIEW PLANE).

New menu button: PLALL, which provides mean-plane (inertial axes) view of molecules currently displayed. (command VIEW IN).

New menu buttons: RX+90 and RY+90, to rotate by +90 degrees about the horizontal and vertical view axes (commands X +90, Y +90).

New menu buttons: HIDEA, DELB, ADDB which have the same effect as typed commands of same name but allow atoms to be selected by clicking.

New commands: Hide link atoms (HIDELA), hide link bonds (HIDELB), restore link atoms and bonds (SHOWL).

New command: EDM +/-n (edit molecule list) to restore/omit molecule from current plot list.

New command: HOME which moves each original molecule to the symmetry-equivalent position in the packing range (0 1 0 1 0 1) where its centroid is closest to the origin.

New command: PLANE n1 n2 n3 draws a plane on the diagram defined by 3 atoms.

New command: VECTOR n1 n2 draws a vector on the diagram defined by 2 atoms

New command: PLANE NONE to delete all vectors and planes.

New command: DOP n1 n2 n3 n4 allows calculation of distance of atom n4 from a plane defined by atoms n1 n2 n3.

New command: COL MOL to colour just one molecule for highlighting.

New command: COL RES to colour one residue for highlighting.

New command: COL DISP which displays the 15 available colours with their code numbers.

New command: COL BOND which highlights a given bond in base molecule with colour code n.

New command: COL PLANE n to colour all planes currently displayed with colour code number n.

New command: COMDEF which sets the default options to be used on RSET and on moving to a new entry. The options are the same as the OPT command.

Modifications

Modification: Plane grid moves appropriately if distance of plane used for packing slice to unit cell origin is changed.

Modification: VIEW IN operates on all atoms displayed in diagram, not just those in the base molecule(s).

Modification: LABL menu button now causes all atoms in a plot, not just those in base set, to be labelled.

Modification: COL SYMM now colours by symmetry operator generating a particular atom, not whole molecule. This allows internal crystallographic symmetry in molecules to be detected readily. Rotational symmetry operators subdivided and LABL SYMM modified to reflect this.

Modification: TITLE command now only applies to the current plot; title is removed on RSET or when moving to a new entry.

Modification: Action of HYDR display toggle (command INCL/EXCL HYD) is now independent of the include settings of the H atoms, i.e. the commands INCL/EXCL H.

Modification: Action of the OPT command is now restricted to only the current entry, on moving to a new entry the options are taken from the COMDEF command if previously given.

Modification: The maximum number of molecules which can be displayed has been increased from 50 to 500.

Modification: COL BOND can now be applied to up to 20 bonds individually. Previously only one bond could be highlighted.

Bug fixes

Bug fix: The STEREO COLour (red-green stereo pair) command, broken in previous releases, has been restored.

Bug fix: Menu highlighting is now correct on RSET or on moving to a new entry. Current settings of LABL and HYDR are retained.

Bug fix: EXCLude/INCLude H now works in a predictable manner. Previously none of the structure was displayed if the EXCL H command was followed by INCL H. The action is now the same as for any other atom type.

Bug fix: CALC (INTRA) now operates correctly after INTER and SPHeRe. Previously, the covalent radius tolerance value was not reset to 0.4 after an intermolecular calculation (vdw radii with tolerance 0.0) so most of the bonds were omitted.

Bug fix: Action of EXP UNDO corrected. Previously, erroneous molecules were drawn in certain circumstances.

Bug fix: Exp toggle is now set correctly when STRT or PACK button selected.

Bug fix: On clicking atom the actual atom selected is labelled (previously the first with the same name in the plot list as that selected was labelled).

Bug fix: SOL/SHAD toggle highlighting corrected to be consistent with molecule rendering.

Bug fix: Incorrect atom labels no longer drawn when maximum number of atoms exceeded.

Bug fix: Improved messages if atom or molecule is outside the packing range of +/- 4 unit cells, if atom, bond or molecule array limits exceeded or unit cell or vectors and planes cannot be drawn.

Bug fix: Improved error messages if command is not recognised or an incorrect number of arguments is given.

Bug fix: Correct handling of packing in multi-residue structures so only atoms in a particular residue, not all the base atoms, are added for each packed residue. This makes more efficient use of atom storage and allows more residues to be displayed before the maximum atom limit is reached.

Known bugs

Known bug: Styles applied to first postscript plot are maintained for complete postscript run.

Known bug: Graph sets cannot be assigned if molecule(s) have internal crystallographic symmetry.

Known bug: Internal crystallographic symmetry ignored by HCAL command so no H atoms are considered as being symmetry-generated.

Known bug: Graph set designators may not all fit on display if a large number of H-bonds are present and designators cannot be shown correctly if motif involves more than 9 donors or acceptors.

Known bug: Bonds may be omitted from molecules if atom plotting limit exceeded.


7. Vista


The Vista program is unchanged since the last release.


8. Gstat


The GSTAT program is unchanged since the last release.


9. PreQuest


The "Copy and Paste" function in PreQuest has been completely re-written this release and a new "Sort" option has been added.

New features

New feature: Sort

PreQuest now has a facility to sort fields within each BCCAB entry. This is intended for users of the 'Edit' command, to assist in navigation around the entry.

If the 'Sort_BCCAB' preference is 'Yes' (in the file "$HOME/.prequest.prf") then the fields will be sorted.

The sort-order is determined by the contents of the file $CSDHOME/csds/prequest.srt.

Users may customise this order, by making a personal copy of the master file, since PreQuest searches in the following list of filenames, and uses the first one it finds:

1. [jobname].srt
2. ./prequest.srt
3. $HOME/prequest.srt
4. $CSDHOME/csds/prequest.srt

New feature: In 3D-Check, a 'HIDE' command has been implemented, to allow selective ommision of residues from the display.

New feature:In 3D-Check, a new command 'HDEL' has been implemented, which deletes all H atoms from atom and bond lists.

New feature:In the file-selection dialog box, the list automatically scrolls to the first file whose name begins with the letter typed.

New feature:In the file-selection dialog box, UP ARROW selects previous entry and DOWN ARROW selects next entry.

Modifications

Modification: Copy...

This command allows information from one entry to be copied on to the PreQuest clipboard.

You may then use the "Paste" command to place the clipboard contents into another entry.

The "Copy Options..." dialog appears, asking you to select which fields are to be copied. Several short-cut buttons save time: 'Deselect All', 'Select All', 'Select 2D' and 'Select 3D'.

As fields are selected and deselected, the first 50 lines of data are accumulated in a scrolling list to show what will be copied.

Fields are listed in the order given in the PreQuest sort file (usually $CSDHOME/csds/prequest.srt, although the user can over-ride this).

Three PreQuest preferences (in the file "$HOME/.prequest.prf") allow the user to customise the behaviour of "Copy...":

  1. 'Copy_Exclude' contains a list of fields which must NEVER be copied from one entry to another. The default is 'ADATE MDATE END'.

  2. 'Copy_2D_fields' contains a list of fields which are copied when you select 'Copy 2D'. The default is 'FORMUL CONN DIAG'.

  3. 'Copy_3D_fields' contains a list of fields which are copied when you select 'Copy 3D'. The default is 'CELL RADIUS TOLER ATOM BOND'.

The 'Copy...' command is not available if PreQuest is awaiting the completion of an external editor session.

Note that PreQuest uses its own internal clipboard, not the X-windows one.

Modification: Paste

This command places the current PreQuest clipboard contents into the current entry.

The "Copy..." command is used to store an entry's formula and chemical diagram in the clipboard.

This command is unavailable if PreQuest is awaiting the completion of an external editor session.

Modification: The LABL menu button in the 3D check menu, now causes all atoms in a plot, not just those in base residues, to be labelled.

Bug fixes

Bug fix: Correct handling of packing in multi-residue structures so only atoms in a particular residue, not all the base atoms, are added for each packed residue. This makes more efficient use of atom storage and allows more residues to be displayed before the maximum atom limit is reached.

Bug fix: Error-checking of the #SATOM field has been improved considerably.

Bug fix: The 3D-Check code no longer issues the erroneous error message 'TOO MANY CRYST. RESIDUES'.

Bug fix: MAKE-2D is now considerably more robust. Previously, large portions of the crystal structure were sometimes ommitted from the resultant 2D diagram.

Bug fix: A bug in the XCOR command has been fixed. This occasionally caused corruption of the #CRYCON field.

Bug fix: PreQuest no longer crashes when reading MacroMolecular CIFs. However, it is still unable to extract any useful information from them. The CIF reading code is also more robust.

Bug fix: The reading and display of ligands and repeats (i.e. -[x]n and -(y)m- ) in chemical diagrams has been improved. The error-checking of chemical diagrams has also been improved,

Bug fix: The CIF reader now extracts crystal source and habit.

Bug fix: The error message: 'The total number of POLYMERIC bonds should be EVEN.' has been removed.

Bug fix:When PreQuest asks for confirmation about whether to save changes to ASER entries, the current refcode is actually displayed.

Bug fix: When the "-auto" option is used, all error and warning messages are now saved in the .lis file. Previously, only the very first message was saved.

Bug fix: In some symmetric structures the NOSYM button in the 3D-check menu could allow entries to be archived apparently without errors, but with the molecule in an incorrect position in the unit cell giving erroneous intermolecular contact distances. This has now been fixed.


10. Planned Changes


We hereby give notice of the following changes to the CSD System (software and data) which we intend to implement in the October 1998 release (version 5.16). These changes are designed to ensure that this and all subsequent versions of the CSD System are Year 2000 compliant.

Expiry Date Mechanism

Currently the CSD System expiry date mechanism uses a routine called idate (in unxtime.c) which returns only a two digit year. In the October 1998 release of the CSD System, the expiry date mechanism will use a new routine which returns a 4 digit year.

ADATE/MDATE

Currently the CSD System stores only two digits for the year in the ADATE (Accession) and MDATE (Modification) fields. The format of these fields is YYMMDD where YY indicates the number of years since 1900. From October 1998, these fields will be extended to store 4 digits for the year, i.e., YYYYMMDD.

As a consequence of this, the following changes will be necessary:

  • QUEST will be changed to read, search and display 8 digit ADATE and MDATE fields

  • QUEST will be changed to output 8 digit ADATE and MDATE fields in ASER and BCCAB files

  • QUEST will be changed to output four digits for the year in the _audit_creation_date data item of CIF files

  • The QUEST Summary file (.sum) will be changed so that each line contains 8 fields of 10 characters (instead of 10 fields of 8 characters) to avoid the extended ADATE and MDATE fields merging with others

  • VISTA will be changed to read, process and display 8 digit ADATE and MDATE fields

  • PreQuest will be changed to generate, read, process, display and output 8 digit ADATE and MDATE

  • conversion routines will be provided to ensure that QUEST, VISTA and PreQuest can handle old datasets that may still contain 6 digit ADATE and MDATE fields

The CSD System currently outputs several fixed-format files that contain ADATE and MDATE. These formats can store only 6 digits for the ADATE and MDATE fields. We have concluded that it is not feasible to change these formats to store 8 digit ADATE and MDATE fields and so they will continue to store 6 digit ADATE and MDATE fields. Whilst this is not ideal, we do not anticipate any problems as a result of this. The earliest ADATE/MDATE field in the CSD is 711231 (31 December, 1971). A unique ADATE/MDATE field will thus be present for all entries added or modified until 30 December, 2071 (711230). We anticipate that the file formats affected will be obsolete by this date. The file formats affected in this way are FBIB, FCON and FDAT.

Any users anticipating problems with this change should contact User Support (support@ccdc.cam.ac.uk) by 31st July 1998.




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