1. CSD in ChemNet (IRIX)

See also the (somewhat outdated) information by Dr. W. Dreißig: Cambridge Structural Database (in German) and the homepage Cambridge Crystallographic Data Centre.

1.1 Starting quest

To run the CSD programs, you have to login to an SGI workstation either directly or via an X terminal.

Start the X Server (X-Win32): Start Programme Internet X-Server, login to your Unix account.

The program used to search the database is called quest.
So try the following: quest

However, this does not yet work, because you have to run a setup program first in order to initiate several variables:

source /software/csdsystem/csdsetup
quest test1

With quest, you have to specify a job name on the command line, in the first example: test1. After starting ``quest'', you have to specify the terminal for interactive work, then you may initiate a few options (e.g., search screens, file types for saving results) and start the menu:

term i
scre 153
save fdat mol2
menu

Then click into the main window.

1.2 First example: Author's Name

Search for structures from the author: H.-U. Reißig.

Menu TO-SEARCH, TEXT..., *SURNAME: reissig(return)
menu TO-SEARCH, FASTQUEST.

Note: Using ``*AUTHOR reissig'' instead of ``*SURNAME reissig'' would also retrieve (e.g.) the author ``Dreißig''. When you get a hit, you have one of the following options: REJECT, KEEP (save and continue) or EXIT. In this example, choose EXIT and answer YES twice.

View coordinate file: rasmol (or raswin)

If your molecular coordinate file has an appropriate type, e.g. Sybyl mol2, you may inspect it by means of rasmol (Unix) or raswin (after downloading the coordinate file to your PC):

rasmol -mol2 test1.mol2

1.3 Second example: (Part of) Compound Name

quest test2

term i
scre 153
save fdat mol2
menu

Menu TO-SEARCH, TEXT..., *NAME: meisenheimer(return)
menu TO-SEARCH, FASTQUEST.

When you get a hit, choose EXIT and answer YES twice.

1.4 Third example: Structure by Template

quest test3

term i
scre 153
save fdat mol2
menu

Submenu TEMPLATES..., 49-Porphyrins, select first (1), click into main window, select FIND-STRUCTURE.

When you get a hit, choose EXIT and answer YES twice.

1.5 Fourth example: Structure (1,3,5-trinitrobenzene)

quest test4

term i
scre 153
save fdat mol2
menu

Select bond type AROM, then RING and specify ``6'', click into the main window. Then attach three nitro groups (with two double-bonded oxygen atoms!) as follows:

Mode MOVE (atom C), click a ring carbon, (mode DRAW) select atom N and bond SINGLE, click at the supposed end of the C-N bond, (mode DRAW) select atom O and bond DOUBLE, click at the supposed end of the N=O bond, mode MOVE, atom N, click at the N atom in your structure, (mode DRAW) select atom O (DOUBLE bond) and click at the supposed end of the second N=O bond. Repeat that procedure for the other two nitro groups (don't forget to select mode MOVE and atom C first!).

Select submenu FIND-STRUCTURE. When you get a hit, choose EXIT and answer YES twice.

1.6 View and measure: mercury

By means of mercury, you can visualize a molecule and measure atom distances, bond angles or torsional angles.

mercury test1.mol2

From the select box Picking Mode, you can choose, e.g., a measuring mode. Style allows you two select a particular display model.

1.7 Converting file types: babel

The program babel allows you to convert an input file (e.g., of type CSD FDAT or SYBYL MOL2) to a different output file type (e.g. Brookhaven PDB, Alchemy MOL or MDL MOL):

babel -m

(Input file type, Choice : ) 13 (CSD FDAT)(return)
(Input file name : ) test1.dat(return)
(Keywords : ) (return)
(Output file type, Choice : ) 44 (PDB)
(Output file name : ) test1.pdb(return)
(Keywords : ) (return)
(Choice : ) 3 (quit)(return)