CSD System Release Notes

April 2000

Table Of Contents

1. Introduction

2. Release Package

3. ConQuest - the new search interface for the CSD (Unix/PC)

4. Database Content

5. Documentation

6. Supported Platforms

7. Graphics Quest3D

8. Pluto

9. Vista

10. Gstat

11. PreQuest

1. Introduction

The CCDC web site is:

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

This site always includes Release Notes and Installation Instructions for the current version of the CSD System and details of any known problems or solutions. For information about the CSD System and the Year 2000 visit our Year 2000 webpages at:

http://www.ccdc.cam.ac.uk/y2k/

Please ensure that any links or references to the old CCDC website - <http://csdvx2.ccdc.cam.ac.uk> - are updated as this URL is no longer active.

If you encounter problems when installing or using the CSD System please contact CCDC User Support by one of the following methods:

Email: support@ccdc.cam.ac.uk

Tel: +44 1223 336022

Fax: +44 1223 336033

User Support, CCDC, 12 Union Road, Cambridge CB2 1EZ. UK

2. Release Package

Your April 2000 UNIX/PC Windows release contains:

This release of the CSD System is supplied on three CD-ROMs:

Database UNIX/PC Windows - the main database files for UNIX and PC Windows platforms.

Software UNIX - Version 5 CSD System Software for all supported UNIX platforms and ConQuest 1.0 for SGI IRIX, Sun Solaris and Linux and various subsidiary database files.

Software PC Windows - ConQuest 1.0 for Windows 95/98/2000/NT 4.x and various subsidiary database files.

3. ConQuest - the new search interface for the CSD (Unix/PC)

ConQuest, the successor to Quest, brings the capabilities of the CSD to PC Windows platforms for the first time.

Licensing of ConQuest:

Please note that ConQuest must be licensed on all supported platforms.

For more information about installation see:

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

ConQuest features:

ConQuest search capabilities:

Additional Information:

ConQuest 1.0 is under evaluation during 2000. It contains almost all of the functionality of Quest and is being onwardly developed. Version 1.1, available in October 2000, will contain additional features. Feedback is welcomed about what you would like to see in future versions. For more information see the ConQuest webpages at:

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

4. Database Content

The statistics for the two release databases are as follows:

Database

Number of entries

Last MDATE

CSD

215,403

20000208

DBUSE

737

20000223

Total

216,140

 

The April 2000 release of the CSD System will expire on 31st December 2000.

5. Documentation

5.1 Installation Notes

The CSD System Installation Notes describe how to install and run the CSD System. They are supplied in hardcopy form and are present in the top level of both Software UNIX and Software PC Windows CD-ROMs as both HTML and plain text files:

and as PostScript and PDF files on the Software UNIX CD-ROM in:

Alternatively, the CSD System Installation Notes can be accessed via the CCDC website at:

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

5.2 Release Notes

The CSD System Release Notes describe the changes that have been made to the CSD System since the last release. They are supplied in electronic form in the top level of the Software UNIX and Software PC Windows CD-ROMs as both HTML and plain text files:

and as PostScript and PDF files on the on the Software UNIX CD-ROM in:

Alternatively the CSD System Release Notes can be accessed via the CCDC website at:

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

5.3 ConQuest 1.0 User Guide

The ConQuest 1.0 User Guide describes in detail all the features of ConQuest 1.0. The document is supplied in hardcopy form and is available via the Help button in ConQuest.

Alternatively, the ConQuest 1.0 User Guide can be accessed via the CCDC website at:

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

5.4 ConQuest 1.0 Tutorials

The ConQuest 1.0 Tutorials are a series of worked examples which illustrate the use of the various features of ConQuest 1.0. They are supplied in hardcopy form and are available via the Help button in ConQuest.

Alternatively, the ConQuest 1.0 Tutorials can be accessed via the CCDC website at:

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

5.5 Version 5 Documentation

Documentation for the Version 5 CSD System Software is supplied on the Software UNIX CD-ROM. The HTML files can be accessed from the top level page:

<CDROM>/html/zdocmain.html

Alternatively the files can be accessed via the CCDC website at:

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

6. Supported Platforms

Version 5 CSD System Software is supplied for the following platforms:

ConQuest 1.0 executables are supplied precompiled for the following platforms:

The Linux version of ConQuest 1.0 has been tested on RedHat 5.2 (2.0.36) and RedHat 6.1 (2.2.12-20) only. If you encounter any problems with other versions of Linux, please let us know.

In addition to the distributed executables, source code for the Version 5 CSD System Software is included on the Software UNIX CD-ROM. This allows users of unsupported UNIX platforms (not listed above) to compile the Version 5 CSD System Software locally.

For information on how to recompile the Version 5 CSD System Software on unsupported platforms, see the CSD System Installation Notes.

The CCDC may not be able to provide full support for any platform not listed above.

7. Graphics Quest3D

Modifications

The Quest program script has been renamed from quest to questv5.

Bug Fixes

It is now possible to search for an H-H bond in Quest, or an XX-H bond where XX is a group definition which includes H.

Implicit hydrogens can be added to an atom XX, where XX is a group definition (ELDEF) which includes H.

Certain searches for water never found coordinated H-O-H, due to a screening problem; this has now been fixed.

Unknown bond types are more easily visible in colour-by-bond mode, when using depth-cueing, by colouring them as light grey rather than dark grey.

Minor corrections have been made to the MOL2 space group symbol table to avoid duplicate symbols; this is used when writing MOL2 output for monoclinic settings with c-axis unique.

The bug whereby molecules were occasionally omitted from packing diagrams is now fixed and the correct translations are calculated for each symmetry operator in turn.

For a few high-symmetry structures the connectivity expansion did not proceed far enough when using the MEXP option of the MECALC feature; this has been corrected.

Total coordination number and spatial coordination number parameters are tabulated correctly for atoms which are symmetry-generated in a nonbonded contact search, by using the coordination number for the atom in the base unit from which each new atom is generated.

8. Pluto

New Features

There is a new command EXCL THYD for hiding H atoms which have only one (intra or intermolecular) connection.

A typed command P(LOT) REFC refcode is now available for moving to a specific refcode when reading data from an FDAT file.

The facility for reading molecule input in Tripos Inc. Sybyl MOL format has been added.

Modifications

In graph set code all intramolecular first-level simple motifs S are given, not just the shortest path involving one donor and one acceptor.

The maximum number of vectors and/or planes which may be displayed has been increased to 96.

When reading MOL2 input, the CRYSIN line is now recognised and the coordinates are transformed from orthogonal to fractional. This does rely on the orthogonal coordinates in the MOL2 file being generated according to the Tripos, Inc. algorithm. Additionally, multiple MOL2 entries can now be read from the same file.

Reading of PDB format is fixed and atoms are transformed from orthogonal to fractional coordinates correctly. The CONECT record is read so that bonds in the PDB file are retained and symmetry-generated atoms are recognised automatically. Additionally, multiple PDB entries can now be read from the same file.

The Atm+/- buttons now scale the radii set with Adef or VdW buttons, rather than using uniform radii.

The condition for adding a molecule centre has changed slightly so that a centre can be added, if other centres are already present, but not if there are intermolecular contacts.

Bug Fixes

The bug that caused a doubled graph set to be given for a ring R when the atoms in the ring lay on a mirror plane, has been fixed.

The shortest ring R is now always included in the final graph set matrix.

The display of second-level composite chain C patterns has been corrected; atoms now appear in a connected sequence without spurious atoms at ends of chain.

The problem of one extra donor and acceptor being counted in second-level composite chain C patterns has been resolved.

The HOME command will now move a molecule into the base unit cell even if the original position was more than three lattice translations from the base unit cell.

Attempting to add methyl hydrogens to a carbon atom, which was only bonded to a terminal atom, was causing HCAL to crash; now no hydrogens are added.

SCK command now works with all input formats; previously it did not work with certain input formats (e.g. BCCAB, MOL2, PDB, CIF).

When reading SHELX input, UNIT, HKLF, SFAC after FVAR and REM (remarks) before END are no longer interpreted erroneously as atom cards.

Space-group recognition, when reading SHELX files, has been improved and if a space group is not recognised then 'x,y,z' the default symmetry is always included.

A vdw radius has now been set for He, Ne and Kr; previously they were given the value 0.0.

9. Vista

The Vista program is unchanged since the last release.

10. Gstat

The GSTAT program is unchanged since the last release.

11. PreQuest

New Features

PreQuest will now read certain variants of PDB files, and PDB has been added to the input formats allowed by the PreQuest startup script; '-ifmt PDB' is recognised.

Modifications

In order to ensure that entries with the same refcode are not archived, when using Export, a warning is now given indicating that this is not possible if wishing to export an ASER file, however, the user is given the choice of omitting or including the entry if exporting another format.

When reading MOL2 files, the CRYSIN line is now interpreted, and, in most cases, the entry presented in fractional coordinates. Previously, the orthogonal coordinates in the MOL2 file were retained.

Bug Fixes

A warning dialogue box is given if an attempt is made to export an entry with the same refcode, already present in the existing ASER database, as well as when updating an ASER entry. Previously this could go unnoticed as a warning was only given in the back window.

The prefixes boro, selan and tellan have been added as allowed prefixes for boron, selenium and tellurium containing crystal structures in the compound name field (#COMPND).

The problem of pi-complexes with fused six and five-membered rings not matching has now been fixed.

The function Intra in the 3d-Check menu continues, even if the contact list is full for a particular atom, previously, no connectivity was generated. A more informative warning message is given with the atom label for the atom with too many contacts.

The space group symbols Fd-3m and Fd-3c have been added to the allowed list.

The problem of entries with space group numbers 221-230 being erroneously archived to an ASER database as non-centrosymmetric has been resolved.

Cambridge Crystallographic Data Centre
http://www.ccdc.cam.ac.uk
General Enquiries: +44 1223 336408
Fax: +44 1223 336033
Support Email: support@ccdc.cam.ac.uk
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