CSD System Release Notes


October 1998 Version 5.16

Table Of Contents

  1. Introduction
  2. Database Content
  3. Software Expiry Date
  4. Documentation
  5. Year 2000 Compliance
  6. Graphics Quest3D
  7. Pluto
  8. Vista
  9. Gstat
  10. PreQuest


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).

The e-mail address for CCDC User Support is:

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 190,307 19980812 PDB Entries 8,084 19980730 CSDS Citations 656 19980902
Total 199,047

The UNIX distribution of the CSDS is now supplied on two CDROMs, Software and Database. The Software CDROM contains the full distribution with the exception of the CSD text-conn-data file (as516be.tcd). The Database CDROM, from which this file can be copied or accessed, contains the files for all three databases (CSD, PDB, DBUSE).

The CCDC distributes PDB data in two formats:

The CSD PDB ASER database contains all 8084 entries released by Brookhaven, on or before 30 July 1998.

The PDB CDROM contains coordinate files for all 6626 entries released by Brookhaven, on or before 30 July 1998, that have been determined by diffraction experiments. Theoretical models and 1458 NMR have been omitted from the PDB CDROM distributed by the CCDC with this release. These entries have been excluded to allow our distribution of PDB coordinates to fit onto one CDROM and a list of the PID codes for the omitted structures can be supplied on request.


3. Software Expiry Date


The UNIX and VMS Packages expire at the end of June 1999.

During June 1999, 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


As announced in the previous release of the CSDS, hard copy release documentation is no longer supplied. Instead, electronic versions of the release documents are provided in three formats (plain text, PostScript and HTML) on your release CDROM.

UNIX users will find Release Notes and Installation Instructions on the Software CDROM in:

	html/zrlnot56.html & zinstall.html (HTML format)
	doc/rn516a4.ps & installa4.ps (A4 PostScript format)
	doc/rn516ul.ps & installul.ps (US Letter PostScript format)
	doc/rn516.txt & install.txt (Plain text format)

VMS users will find Release Notes and Installation Instructions in:

HTML format

	CDROM:[dbase.release.doc.html]zrlnot56.html
	CDROM:[dbase.release.doc.html]zinstall.html
A4 PostScript format
	CDROM:[dbase.release.doc]release_notes_v516_a4.ps
	CDROM:[dbase.release.doc]installation_notes_v516_a4.ps
US letter format
	CDROM:[dbase.release.doc]release_notes_v516_usl.ps
	CDROM:[dbase.release.doc]installation_notes_v516_usl.ps
Plain text format
	CDROM:[dbase.release.doc]release_notes_v516.txt
	CDROM:[dbase.release.doc]installation_notes_v516.txt

All of these documents can also be accessed via the CCDC website at:

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


5. Year 2000 Compliance


The changes to the CSDS expiry date mechanism, the accession date (ADATE) and modification date (MDATE) records, announced in the April 1998 Release Notes, have now been implemented. These changes ensure that this release (version 5.16) and all subsequent versions of the CSDS are year 2000 compliant.

5.1. How These Changes Affect Saved Database Subsets

QUEST will automatically convert database entries in the old (YYMMDD) format into the new (YYYYMMDD) format as it reads them. Since the conversion process has little impact on search speeds there is no advantage to reformatting database files prior to searching. In the UNIX release a conversion routine called cnvrt98 is supplied for users who require reformatted database files for other purposes.

cnvrt98 requires two database names. The input database (in the old format) is not modified. All entries are read, and saved to the output database in the new format.

	% cnvrt98 [-if] inputdatabase [-of] outputdatabase

For more information about cnvrt98, type:

	% man cnvrt98

VMS users can use the CSDCONVERT utility to extract a refcode list from a subset. This refcode list can then either be used to create a new subset or, preferably, used to create a virtual database. For more information about the CSDCONVERT utility type:

	$ CSDHELP CSDCONVERT

5.2. Testing Year 2000 Compliance

In order that users may have the ability to test the year 2000 compliance of this release of the CSDS, a small database subset containing entries with ADATEs and MDATEs ranging from 1998 to 2009 has been included. The database, which is located in $CSDHOME/examples (UNIX) or CSDROOT:[RELEASE.TEST.Y2K] (VMS), is called y2k. Full instructions for accessing the y2k database are given in both the UNIX and VMS Installation Notes.


6. Graphics Quest3D


New features

New feature: 'SAVE CIF' now writes out '_chemical_formula_sum' for compatability with the IUCr's cif2sx program.

Bug fixes

Bug fix: 'TOTAL COORD NO's greater than 9 can now be defined via the 2D-CONSTRAIN Menu in the graphical interface. Previously, it was only possible to define two digit 'TOTAL COORD NO's via the command line.

Bug fix: Improved error message handling now prevents endless lists of certain common error messages being generated during searches.

Bug fix: 'FORMULA' searches involving the element type HD (hydrogen or deuterium) now retrieve deuterated, as well as hydrogenated, entries.


7. Pluto


New features

New feature: Geom button, which provides the interface to the CENT, PLANE and VECT commands, allowing geometric objects to be defined by selecting atoms.

New feature: HideM button, which acts as a graphical interface to the EDM command, allowing molecules to be hidden, grey-shaded and restored by selecting the appropriate atoms in packing diagrams. This provides an alternative method of selecting a group of molecules to the Expand function.

New feature: the distance between an atom and a plane can be found by selecting the labelled corner of the plane and an atom (command DOP PL pl1 at1).

New feature: conventional graph set descriptions are now written to the command window in matrix form (120-column format).

New feature: CENT command, which adds the centroid of a number of atoms as a dummy point to atom list.

Modifications

Modification: residues in the base set are now plotted as separate molecules with sequential numbers in the molecule list. These molecules are included in packing diagrams if they lie within the packing box, improving the efficiency of atom storage when Pack is on.

Modification: distances between atoms defining a plane and the plane are now given in the command window when a plane is defined.

Modification: clicking on EXP twice, rather than on a link atom, causes expansion to occur on all active links (as EXP ALL command) which is useful for rapid expansion of H-bonded chains and sheets.

Modification: planes are now labelled with their plane number.

Modification: Plane and PlAll have been replaced with a combined Vp (view plane) button.

Modification: graph sets can be defined for non-bonded contacts other than H-bonds by using the command GSET DON donor atoms ACC acceptor atoms, in addition to the basic command GSET for H-bonds.

Modification: graph sets may now be determined in most cases where molecules have internal crystallographic symmetry.

Modification: directionality of contacts in second-level graph sets are now indicated in the key.

Modification: bonds, as well as atoms, are coloured in Solid mode for COL SYMM, COL MOL and COL RES options.

Modification: current character size and linewidth may be retained on Rset and Next if STYLE is present in the COMDEF default settings command.

Modification: (UNIX only) the user may specify the filename for postscript output, checks are carried out to ensure that the file does not already exist and, if it does, the user is prompted as to whether or not it should be overwritten.

Bug fixes

Bug fix: problem corrected where some atoms are outside the plot boundary after re-sizing the plot, by scaling the diagram after applying rotation matrix.

Bug fix: colour key can be scrolled so that all graph set designators may be shown, the space in the key has been increased so that graph sets with more than 9 donors or acceptors are displayed correctly, and key text is scaled if the character size is changed.

Bug fix: operation of Sphr and Inter functions has been corrected so that they may be used to generate contacts for graph set analysis, by avoiding duplicate link atoms and bonds.

Bug fix: command CALC INTER RAD element1 behaved as Sphr calculation if only one atom of element1 was present.

Bug fix: molecules are no longer omitted from packing diagrams if two base residues share the same centroid (e.g. host-guest compounds).

Bug fix: labels are now placed correctly in Solid mode if the character size is changed.

Bug fix: no longer turn all labels on with INCL ALL command.

Bug fix: Nbo+/- no longer correlated with Bon+/- setting.

Bug fix: ensured that a cross is drawn to indicate the atom position even if it has no bonds currently displayed.

Bug fix: efficiency of fast-rotation buttons has been improved and atom and bond lists are no longer set up for every plot.

Bug fix: FDAT files with more than 600 characters in text fields can now be read, although only the first 640 are stored.

Bug fix: Title is shown correctly when reading from free-format input.

Bug fix: no longer crashes in ASSIGN command and Hbond function where there are more than 10 connections to an atom (e.g. in disordered structures).

Bug fix: bond distance removed from the display if the bond is deleted.

Bug fix: additional contacts can now be defined after 'retaining current contacts' option is selected in Hbond calculations.

Bug fix: Graph set function now operates correctly with free-format input.


8. Vista


The Vista program is unchanged since the last release.


9. Gstat


The GSTAT program is unchanged since the last release.


10. PreQuest


New features

(None)

Modifications

Modification: menu button SIZE has been added to the 3D Check menu to allow the plot to be scaled to the view area; this is done automatically after certain operations.

Modification: POLYM now offers more options for the expansion of polymeric structures. Option 10 is for (experimental) expansion of complete ligands around metals, options 18 and 19 are alternatives to 8 and 9 but they do not restore previously deleted bonds. Options 4 and 5 have been removed from the list as they are not routinely used, although are still accessible by entering the appropriate number at the prompt.

Modification: improvements have been made to the polymer select-by-2D diagram option POLYM 2. The coordination number of atoms in 2D and 3D match exactly unless the 2D atom has only polymeric (bond type 6) bonds, and the base atoms in the 3D are not matched to the atom in 2D with only polymeric bonds.

Modification: MATCH now treats D the same way as H for the purposes of matching, which allows residues to match if D atoms are missing from the 3D connectivity.

Modification: Entries will now match if there are two 2D residues which differ only in charge or the number of terminal H or D.

Modification: warning message has been added if there are more than 30 connections to an atom, as this prevents the structure from being saved in ASER format.

Modification: AddB and DelB now apply to all symmetry-related bonds.

Modification: formula of crystal (3D) residues is reported with MATCH even if no 2D diagram present.

Modification: Info button now reports current values of #RADIUS and #TOLER.

Bug fixes

Bug fix: large structures with up to 1500 bonds are allowed to connect properly (previously structures with more than 750 bonds did not show any bonds at all) and prevent bonds being lost by increasing the allowed number of CRYCON integers.

Bug fix: bonds are prevented from being added more than once with the AddB button.

Bug fix: connectivity is now preserved on Quit and Save after POLYM options 1 and 3.

Bug fix: operation of POLYM 2 option has been corrected where more than one 2D or 3D residue is present.

Bug fix: POLYM 2 option now works correctly where bridging H or D atoms are present in the 2D and 3D connectivity.

Bug fix: ensured atoms selected by POLYM 2 option are in the appropriate coordinate range.

Bug fix: Atom labels no longer appear as ??????? after certain polymer options.

Bug fix: POLYM options 8 and 9 now add all links; previously some were omitted.

Bug fix: problem has been corrected where some atoms are outside the plot boundary after re-sizing the plot, by scaling the diagram after applying rotation matrix.

Bug fix: MATCH now works correctly if some atoms are not displayed (e.g. if some residues are hidden or hydrogens are not displayed).

Bug fix: structures with H-H bonds now match correctly.

Bug fix: bonds are now highlighted correctly with MFIX function.

Bug fix: Residue/Pick selection no longer lost on subsequent rotation after MATCH has been attempted.

Bug fix: efficiency of fast-rotation buttons has been improved and atom and bond lists are no longer set up for every plot.

Bug fix: erroneous atoms are no longer displayed when Resi or Pick is active and some symmetry atoms are lost after suppressing base atoms.

Bug fix: molecules are no longer omitted from packing diagrams if two base residues share the same centroid (e.g. host-guest compounds).

Bug fix: corrected operation of automatic radius adjustment based on author's bonds. Previously the radius change needed could be overestimated or the tolerance value set incorrectly, or initial radius set to 0.00 for some atom labels.

Bug fix: no longer crashes in XCOR if too many bond angles are entered .

Bug fix: no longer crashes with ASSIGN command and MAKE2D function where there are more than 10 connections to an atom (e.g. in disordered structures).

Bug fix: cent flag and #SYMM lines are reset in BCCAB file if the cent flag is inconsistent with the space group symbol.




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