This example uses example Cimetidine data from the EXPO software
|Now assuming you have an acceptable cell and spacegroup, it is time to try and make sure we are not re-inventing the wheel in trying to solve a structure that is already known.|
If you are already running platon on a UNIX computer where the CSD and Quest
already been installed, this is extremely trivial.
Note: If searching on a cell obtained from Powder diffraction data, and you do not get any hits. It is advisable to edit the *.QUE file and change the tolerance from 0.01 to 0.05 (or some value that makes you happy). In this tutorial, we will be setting the tolerance via Platon to 0.05.
In this example we will deal with the case where the user is on a Windows PC, and the CSD database is on a remote UNIX machine where Platon has been compiled. (it is possible to generate the Quest query on Platon for Windows and ftp it over to run manually in quest - using a command line similar to quest -j structure_name < structure_name.que)
NOTE: With quest, make sure it is not automatically going into Xterm/Menu mode or the following will not work. By default, Quest should not go into Xterm/Menu mode but the administrator may have set it up like this to save on a few keystrokes.
If you have not done already, information on settup up for Secure FTP and Secure X sessions from a Windows machine, refer:
If a UK based academic or student, you can obtain free and easy access to the Cambridge and other structure databases via the EPSRC funded CDS - Chemical Database Service (free registration is done On-line)
Following is the cell information we have on the sample in Shelx INS format which
Platon/System S users. The chemical, spacegroup
and other information is superfluous in the case of this search. (note that there is
no spacegroup information in this System S starting file)
FTP the starting INS file to the remote machine. In this case the Chemical Database Service server (freely available after registration for any UK based academic or student) at cds.dl.ac.uk. (you will need your CDS username and password handy to do this)
Run teraterm and login to the UNIX computer containing the Cambridge database
(in this case cds.dl.ac.uk).
Run your Windows X-server (in this case the MI/XServer for Windows)
In the teraterm shell, go to the directory where the Shelx INS file with the starting information is, then type platon cime.ins. This will spawn the following window in your windows X-server.
To redraw a screen if you swapped into a Window program, just use CONTROL L.
We wish the CELL searching tolerance to be increased from 0.01 to 0.05.
In the bottom left Platon command line, type set parm 28 0.05 and press Enter to achieve this.
Under the MISC-TOOLS option, select CSD-CELL and Platon will
generate the Quest file then try and spawn Quest if this is available locally.
If you swap into the Teraterm screen, you can see Quest running and it has found
Platon will now display the structures that were found graphically. In the present July 15th 2000 version
of Platon, use the bottom right PREV and NEXT menu options to browse the found structures.
In this case, it has found that the structure has already been solved. But this will not stop up continuing onward in the of contrived web tutorials!
If platon tells you it got hits (on the bottom left of the screen) but does not give display a structure, but gives the following output at the bottom right of the screen. It could be there is a nuance with Platon and the Windows X-server in being able to spawn extra screens. Look manually in the Quest files, and these will tell you want structures it found.
Even if things go well, you can of course view manually the jnl journal file.
You can do the following manually in Quest by copying the QUE file
generated by Platon to a machine with Quest on it and run quest and import the file.
quest -j structure_name < structure_name.que
QUEST Query file