How to get connected to the CSD and start
a basic search
On-line
documentation for searching the CSD
Go to X-ray Info Index
For assistance and questions, please contact Dr. A. Linden (Tel: 5 42 28)
Please delete all unwanted search files when you are finished with them.
The information provided here is intended primarily for members of the Institute of Organic Chemistry. Users at other sites may need to employ slightly different commands to start the search program and other applications, because some of the commands have been locally personalised or are installation and platform specific.
The new interface is quite intuitive. If you try the various options, you should quickly learn how to construct queries, perform searches and analyse the results. Interactive help and tutorials are available and the on-line manuals should be consulted for detailed information.
Detailed on-line documentation is available. Help is also available during a search, as each window has a HELP menu or button.
If the manuals do not resolve a question, Dr. Linden is always available to assist you. He can also help with any questions that you might have about search strategies.
Before you start, if you wish to keep the current search results separate from another search, create a new subdirectory for each search with the command mkdir xxxx, then move to the subdirectory with the command cd xxxx.
questv5 project
where project is your projectname. All files subsequently created will carry this name.
When the questv5 command is issued, some information will be displayed and after a few seconds the terminal will enter the graphics mode and you may start developing your search questions. If you are using VersatermPro and have trouble using the mouse, or the crosshairs do not appear, check that the type of terminal emulation chosen when you logged in corresponds to the actual graphics emulation at your terminal.
When building a structure, use 2D-CONSTRAIN to define hydrogen atoms, otherwise other connections will be tested. 3D-CONSTRAIN can be used to define geometrical tests for the search, so that these features can be analysed in a histogram or a scattergram, or used later in the structure analysis program vista. When you have finished creating a search fragment and defining the desired features, use DEFINE STRUCTURE to produce the search question.
If you want to create tables of bond lengths, angles or torsion angles, select the desired tables from the GLIST section of the SEARCH Menu. If you want the Bibliography file to contain additional information, the Postscript file to be in a different format, or additional types of files to be saved, select the appropriate options from the SAVE and PRINT sections of the SEARCH Menu. The default settings should be adequate for most searches.
Several questions can be built up before selecting QUEST to do the search. Search questions do not have to be solely based on structural fragments. Text and numeric strings, such as authors' names, compound names, formula and year are a few examples of possible options. Click on TO SEARCH to bring up the SEARCH Menu if you want to use these options.
When QUEST is selected you must click on the graphic display for each part of the question that you want to include. You must also click on a command to combine multiple questions. e.g. use .AND. .OR. etc. You may also specify at this point various options, such as to display only error-free data, or only structures for which atomic coordinates are available, or only organic structures, etc. Then click on START-SEARCH.
During the search, hits will be displayed and you can keep or reject them. A question that is too general could give a very large number of hits. Many other options are also available, including on-screen rotations of a 3D view of the structure (select 'To 3D') and the ability to find bond lengths, angles and torsion angles just by clicking on the relevant atoms. Try selecting all of the different options to see what is possible.
IMPORTANT: When the search finishes, answer Y to the exit question or else the hits will be deleted! However, if you have discovered that your initial search fragment was producing the wrong results, answering N to this question and will return you to the Build Menu where you can modify your search structure; if you exit, the search structure will have to be built again from the beginning.
| project.jnl | Bibliography for all kept hits. |
| project.dat | Crystal data and atomic coordinates for all kept hits. |
| project.ps | PostScript file containing the structural diagram and the bibliographic data for each hit. An example is given on the following page. |
| project.gls | Bond lengths, angles and torsion angles for all kept hits. Only present if one or more of the options from the GLIST section of the SEARCH Menu were selected. |
| project.sum | Present only if the 3D-CONSTRAIN Menu was used and contains a summary of the geometrical results. This file will contain the histograms or scattergrams if they were requested. To understand the symbols, consult the file "project.fgd". |
Other files may be produced if you select special options. A directory listing (with ls -l) will show you all of the files created. Some special files may be in binary and are therefore unreadable.
The PostScript file, project.ps, is probably the most useful record of what you have found, however, if you want a listing of the bibliographic entries without a structural diagram, the bibliography file project.jnl is the one to use.
If you are not interested in actually working with the atomic coordinates of the structures that you have found, then a printout of one or more of the above files is all you will need. To print a file, first transfer the file to your local workstation or a Macintosh using FTP (on a Macintosh the FETCH utility is recommended). The PostScript file can be printed on a Macintosh by dragging it directly to a desktop printer icon, or with Drop*PS (a nice utility for printing PostScript files).
cq -j project (you can also use conquest project)
where project is your projectname. All files subsequently created will carry this name.
When the cq command is issued, some information will be displayed in a small window and then the main window will apppear. Be patient as the startup may take quite some time. From the list of buttons on the left side select the Draw option to sketch a molecule and a new window will be displayed, while the other options allow you to enter various text or numerical information to search on.
In the Draw window, the ADD-3D option can be used to define geometrical tests for the search, so that these features can be analysed, or used later in the structure analysis program vista. When drawing a fragment, remember that H-atoms are not implicit and you must define them to complete an atom's valency if you do not wish to find all structures with ANY substituent at the incomplete site(s).
Several questions can be built up before starting the search. Search questions do not have to be based solely on structural fragments. Text and numeric strings, such as authors' names, compound names, formula and year are a few examples of possible options. If you wish to develop multiple queries, choose the Store option after creating each individual query (choosing the Search option will start a search directly using the current query only). Multiple questions can be combined using the Combine Queries tab in the main window, e.g. with AND, OR, NOT, etc. You may also specify various options, such as to display only error-free data, or only structures for which atomic coordinates are available, or only organic structures, etc.
Further information is available in the comprehensive on-line documentation.
Search results will not be saved unless this is specifically requested (you will be warned if you attempt to exit without saving anything). A choice of different file types with varying information content is available. Unfortunately, the old option of obtaining a PostScript sketch listing of the hit structures is not available in the current version of ConQuest.
vista -j project
It is then possible to get a graphical analysis for various geometrical features, or to graphically look at the information available individually for each entry in the same way that the hits could be viewed during the original search. Thus it is possible to view the molecule in 3D and to rotate it on the screen, as well as look at individual bonding parameters. The full bibliographic data can also be viewed on the 1D screen.
The program pluto can be used to view, rotate, draw, analyse and perform mechanics calculations on the structures you saved during the search. This is more flexible and powerful than the 3D viewer available during the search itself. Start the program with the command:
pluto project
format
The program should be self explanatory - choose option 10 (Cambridge FDAT file) for the input format. One file will be created for each structure that was in project.dat, with the file name corresponding to the Coden for the structure (Codens are given in the bibliographic listing). For example, if you selected Ball & Stick format, the file name extension will be .bs.
The program format is not part of the CSD installation and is only installed locally. If you are an external CSD user and you would like a copy of the Fortran source code, please e-mail a request to alinden@oci.unizh.ch. The program is currently running under VMS and Unix.