C637:  Introduction to Cambridge Structural Database

Before you start the tutorial, please read the CSD application note which outlines the Cambridge Structural Database (CSD) and the ConQuest program. You may consult this note and the online ConQuest documentation on the CCDC web site during the tutorial . You are also encouraged to go through the online ConQuest tutorials on the CCDC web site. Moreover, a local copy of the ConQuest documentation and the ConQuest tutorials is also accessible for the departmental SGI computers.

This page contains some contents that came from the CCDC's CSD documents.

• Getting Started
• Chemical Formula Search
  • Chemical formula search
  • Save 3D coordinates
  • Save and print search results
  • Save and read searches
• Substructure Search
• Author/Journal Search
  • Author/journal search
  • Edit, delete, save, and read queries
• Combined Compound Name & Keyword Search
• View 3D Structure
  • Move molecules
  • Change molecular display styles
  • Label atoms
  • Measure distances, angles, and torsion angles
  • Display crystallographic unit-cell contents

1. Login to your account on one of the departmental SGI workstations.
2. Open a UNIX shell: Click the left mouse button on Desktop in the toolchest (in the top left corner of the screen), then click on UNIX shell in the new pop-up menu.
3. In the UNIX shell (with the mouse cursor positioned in the UNIX shell), type cd to go to the appropriate directory. (If you are not familiar with UNIX, take a look at the UNIXhelp on-line manual and the UNIX commands quick list).
4. Type cq to start ConQuest.
5. Take a few minutes to familiarize yourself with the layout of ConQuest. In particular, note the following:
   • Most selections are performed by a single click with the left mouse button.
   • Searches for text are not case sensitive, i.e. it does not matter whether upper or lower case is used. However, when you specify UNIX files and directories, those texts are case-sensitive.
   • Before typing text into an input box, the box should be activated by clicking on that box.
   • For most input boxes, the color will become pink if the input is invalid.
   • Buttons are inactivated (gray colored) when they cannot be used. This is usually because the user has not provided sufficient information for these buttons.
   • Most dialogue windows have the following four buttons:
     • Search - starts a search with the query that has been defined in the dialogue window, then closes the window and store the query in the Build Queries and Combine Queries screens.
     • Store - stores the query in the Build Queries and Combine Queries screens without starting a search, and closes the dialogue window.
     • Cancel - cancels all inputs and closes the dialogue window.
     • Reset - deletes all input but leaves the dialogue window open.
6. Click on the View Databases icon in the top menu to browse all CSD data entries in alphabetical order.
7. Click on the Help icon on the top menu, then click Help Index or Tutorials in the following pop-up menu to see the online ConQuest manual or Tutorials. This will start the Netscape browser.
8. Click on File and then Exit to exit the program. If you have performed searches, the program will remind you to save those searches before exit.

1. Start ConQuest.
2. Hit the Formula button, the Formula dialogue window will open.
3. Type a chemical formula (e.g., c6h12o6) into the Formula box.
   • Any space you type in will be ignored by the program.
   • Text you type in is not case sensitive e.g., no matter you type C19H16Fe1O2 or c19h16fE1O2.
   • A element symbol must be followed by a number e.g., C19H16FeO2 is invalid; you should type C19H16Fe1O2 instead.
   • The formula can be exact e.g., C12O4H18, or inexact e.g., C6-8O>2 (which means 6, 7 or 8 carbon atoms, and more than 2 oxygen atoms).
   • Element group symbols can be used, which must be enclosed in square brackets e.g., C6[7A]2, where 7A means any halogen atom.
   • You can set up a formula from the Periodic Table.
4. Click on one of the diamond shaped buttons to specify whether the formula applies to an individual molecule or all the molecules in the structure added together. For example, the crystal structure acetylcholine perchlorate contains two individual ions with formulae C7H16N1O2 (acetylcholine) and Cl1O4 (perchlorate), the formula of the individual ions added together is C7H16N1O6Cl1.
5. Specify whether other atoms allowed in molecule/structure, apart from those defined in the formula (click on the square button to switch on (red color) or off).
6. Hit the Search button in the Formula dialogue window. The Search Setup dialogue window will be opened, in which you can:
   • Name the search by typing into the search name box.
   • Elect to run the search on a subset of the CSD, or on an in-house database of crystal structures (not yet available).
   • Select filters (e.g., reject disordered structures, reject polymers).
   • Select Reset to return to the status of the Search Setup dialogue window when first displayed.
7. Hit the Start Search button in the Search Setup dialogue window, the search will be started and the screen is automatically switched to View Results. After a while, the refcodes of hit entries start to appear in the hit list box on the right part of the View Results screen. The structural diagram of the first hit refcode is shown in the main box of the View Results screen. Click on the tabs on the left side of the View Results screen to see other information e.g., author/journal, crystal, chemical, etc.. Click on another hit refcode listed in the hit list box to retrieve associated information.
8. You can stop the search by hitting the Stop Search button under the hit list box. A pop-up window will ask for your confirmation.
9. Unwanted hits may be suppressed by clicking on the green checkmark prior to the refcode in the hit list box. Those refcodes, now marked with a red cross, will not be written to your export file. Clicking on the red cross will turn it back to a green checkmark.
10. To save the 3D coordinates of the hit structures:
    • Ensure that the View Results screen is active (if not, click on the View Results tab).
    • Click on File in the top-level menu and select Export Entries as ... from the pull-down menu.
    • Click on the file type bar and select one of the following file formats, that can be handled by the other software you will use (e.g., Cerius²) from the pull-down menu: CIF, CIFMIF, COORD, FDAT, MOL2, PDB. (Select FDAT for Cerius²).
    • Save the individual structure currently being displayed (turn on Current entry only) or all unsuppressed structures in the hit list (turn on All selected entries).
    • Some options need to be specified for some formats e.g., if you want to save more than one structure in PDB format, either an individual PDB file will be created for each structure (One file per entry) or all structures will be combined in a single PDB file (Concatenated).
    • Enter an output file name in the file name box (if you don't specify a name, a default name will be used).
    • Hit save next to the file name box.
11. To save and print search results:
    • Search results (diagrams, literature references, etc.) can be saved as PDF files, that can then be viewed and printed with Acroread (In UNIX shell, Acroread with a -toPostScript option can convert PDF to PostScript):
      1. In the View Results screen, select File from the top-level menu and Write PDF file to view/print... from the following pull-down menu.
      2. Use the buttons prior to each item and option in the Write PDF File dialogue box to control the contents of the PDF file e.g., number of entries per page, which items (diagram, journal reference, etc.) should be included, whether information should be kept for the structure currently displayed or for all unsuppressed structures in the hit list.
      3. Enter an output file name in the file name box or use the default name, then hit Write next to the file name box.
      4. A pop-up window will ask whether you want to View PDF file now? Clicking yes will open the PDF file with Acroread. You can print the file with Acroread.
    • Alternatively, search results (except diagrams) can be saved into as TXT files, which can then be viewed, edited and printed using general UNIX commands:
      1. In the View Results screen, select File from the top-level menu and Export Entries as ... from the following pull-down menu.
      2. Click on the file type bar and select TXT: text representation from the pull-down menu.
      3. Select items and options; enter a file name (or use the default name), then hit Save.
12. To save and read searches:
    • Ensure that the View Results screen is active.
    • Click on File in the top-level menu and select Save Search (only available if the search has already been saved) or Save Search as ... in the following pull-down menu.
    • Enter a file name into the file name box on the pop-up Save Search window (or use the default name). All search files are given the extension .cqs by default.
    • Hit Save next to the file name box, the most recent search (which is currently displayed on the View Results screen) will be saved. The search file is binary and contains all the information necessary to read the search back into ConQuest and display it as if it had just been run.
    • To read a previously saved search, click on File in the top-level menu and Open Search ... in the following pull-down menu. If this option is used when there are already queries in the Build Queries screen, a new ConQuest window will be opened for the retrieved search.

See the online ConQuest tutorials on the CCDC web site.

1. Start ConQuest.
2. Hit the Author/Journal button, Author/Journal dialogue window will appear.
3. Type an author's name (e.g. k.g.caulton) into the Authors' Names box.
   • No spaces are allowed between the initials and the surname.
   • The search is not case sensitive e.g., search for K.G.Caulton will get the same results as for k.g.caulton.
   • You have to use the initials that were used by the authors in the paper (authors' names in the CSD are same as appeared in the paper) e.g., a search for k.caulton will get nothing. More than one search using different initials, or using just the surname should be carried out if you are not sure about initials.
   • Only one name can be submitted per box. If you want to specify the co-authors (e.g. j.c.huffman), click on the New Box button then type them in the newly opened Authors' Names boxes.
4. Hit the Search button in the Author/Journal dialogue window, then the Start Search button in the next window, the search will be started.
5. Wait for the search finishing (282 hits for K. G. Caulton, 1147 hits for J. C. Huffman, wow!!!), or hit the Stop Search button in the View Results screen to stop the search.
6. Click on the Author/Journal button in the View Results screen to display the literature citation of the hit entries.

7. Click on the Build Queries tab to switch to the Build Queries screen, then click on the Edit... button in the Query 1 box (which was previously used for the author name search), the Author/Journal dialogue window will appear again and the previous typed-in author names are still in the Authors' Names boxes.
8. Type the first few letters of the journal (e.g., ino for Inorganic Chemistry) in the Journal Name box, journals beginning with these letters will be shown in the journal list box. Select the journal name which you want to specify (e.g. Inorg.Chem.) from the list by clicking on it.
9. Hit the Search button in the Author/Journal dialogue window. The question "Overwrite existing Query?" will be prompted, answer with yes and then hit Start Search in the next window to start  the new search.

To delete a query:

Switch to Build Queries or Combine Queries screen and click on Delete next to the query to be deleted. To undo this action, click on Edit in the top-level menu bar and Undelete Queries in the following pull-down menu.

To save queries:

At Build Queries or Combine Queries screen, click on File in the top-level menu bar and Save Queries in the following pull-down menu. It is then possible to save either one particular query or all queries (in a single file).

To read queries:

At Build Queries or Combine Queries screen, click on File in the top-level menu bar and Read Queries... in the following pull-down menu, then select the query file in the pop-up Read Queries window and hit open (queries are stored in files with the extension .qry by default).

See the online ConQuest tutorials on the CCDC web site.

Hit the 3D Visualiser button in the View Results screen to see the currently selected structure in 3D. The molecule can be moved by using the mouse buttons. Clicking the right mouse button anywhere in the 3D window will open a control menu which can be used to select various options.

• Rotate the molecule by moving the cursor around in the 3D window while keeping the left mouse button pressed.
• Rotate the molecule about the z-axis (the axis perpendicular to the screen) by moving the cursor while keeping the left-hand mouse button and the Shift key pressed.
• Shift the molecule by moving the cursor in the 3D window with the center mouse button pressed.
• Move the cursor up and down in the 3D window with the right mouse button pressed to zoom in or out.
• To reset the molecular view, right-click to open the control menu and select Reset View.

Four display styles -- wireframe, capped stick, ball-and-stick and space-filling, can be chosen for rendering molecules. Hydrogen atoms can be displayed or hidden.

• To change the display style of the whole molecule or unit cell, right-click to open the control menu, click on Display and then pick the chosen style.
• To change the style of a few atoms, select them by clicking on them with the left mouse button while keeping the Shift key pressed down. Then right-click to open the control menu, hit Display and pick the required style.
• Drag the right mouse button while keeping the Shift key pressed to change the viewing perspective i.e., change from orthogonal projection (the default) to perspective projection with increasingly large viewing angles.
• Hydrogen atoms can be displayed or hidden: right-click to open the control menu and turn Display Hydrogens on or off

• Right-click to open the control menu and select Label. You have four choices: No Labels, All Atoms, No C,H,N or O (all atoms except C, H, N and O), and Selected (selected atoms).
• If you choose Selected, select the particular atoms you want labeled by clicking on them with the left mouse button while keeping the Shift key pressed down.

• Ensure that no atoms are currently selected (a selected atom is marked by a yellow dot). To remove the atom selections, click on an atom with the left mouse button (only this atom is selected and all other atom selections are lost), then click on this atom again with the left mouse button while keeping the Shift key pressed down (i.e. unselect this atom).
• Right-click to open the control menu, select either Measure or Picking Mode from the menu, then select either Pick Distances, Pick Angles or Pick Torsions in the following pull-down menu.
• Depending on the mode that was chosen, click on two, three, or four atoms, respectively, to measure the distance, angle, or torsion angle.
• To leave of the measurement mode, right-click to open the control menu and select Measure followed by Default Picking Mode.
• To clean the measurements from the display, right-click to open the control menu and select Clear Measurements.

• Right-click to open the control menu and select Packing, then select 1 Unit Cell from the following pull-down menu.
• To display only one molecule, right-click to open the control menu and select Packing followed by Molecule.

Log out of your account:

Click on Desktop in the toolchest then Log out in the pull-down menu. OR, position the cursor in the background area of the screen, Click & hold the right mouse button, and select Log Out. FOR SECURITY REASONS, DO ALWAYS LOG OUT !!!