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Tutorials and Examples

Platon (Shelx Compatible) Structure Analysis Toolkit Software by Ton Spek

CSD (Cambridge Structure Database) Cell searching - Using Platon as a user-friendly interface into Quest

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Tutorials page] | [Platon Tutorial Index]
[Platon Introduction] | [Obtaining Platon] | [Installing and Running Platon] | [Starting out with Platon] | [Runthroughs of some Platon functionaltiy]
[Platon CSD Cell Searching] | [Platon CSD Related Structure Searching] | [Platon - Generating CSD Quest Scripts for later use]

Another mega-powerful time saving feature of platon is the ability to act as a user-friendly interface for the Cambridge Database Quest program to search on related organic and organometallic phases. Which thus offers the ability to easily determine if the structure has already been solved via giving it the cell, or "your" solved structure.

In the following case, we will give Platon the cell information of an organic phase to see if the structure may have already been solved.

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; then manually run Quest. This is described in more detail at the bottom of this tutorial.

Here 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)

The following example is from the sdemo.ins example given with Platon in System S mode to demonstrate the NQA (no questions asked) mode of System S.

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. 

TITL SDEMO
CELL 0.71073 4.0007     7.7300    16.7597    90.0540    94.0760    90.0528    
ZERR  2  0.0010     0.0008     0.0022     0.0096     0.0160     0.0144         
SFAC C H O
UNIT 10 12 6
HKLF 4

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 filename.ins. This will spawn the following window in your windows X-server. (The relevant parts of the menu for searching via Quest are circled)

Running a UNIX Platon via a Windows X-server

To redraw a screen if you swapped into a Window program, just use CONTROL L.

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 a hit!

Searching the Cambridge Database via Platon Spawning a command line Quest session

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 option to scroll through the found structures.

Platon graphically presents the results from the cell search on the screen

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.

(Note: If searching on a cell obtained from Powder diffraction data, and you do not get any hits: It is advisable to increase the tolerance. There are one of two ways of doing this:

  1. In Platon: Use the command SET PAR 28 0.05 (the bottom of the Platon graphics screen has a command line option) to in this case change the tolerance Platon will use for generating Quest scripts from the default of 0.01 to 0.05.

  2. Edit the Quest Script Directly: Edit the platon generated *.QUE file and change the tolerance (located after the cell information) from 0.01 to 0.05; then manually run Quest using the above command.)
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 
SAVE 3
T1 *PCELL    TRICLINIC    4.001    7.730   16.760  90.05  94.08  90.05 0.010
QUESTION T1

Resulting Journal File 
COMM +----------------------------------------------------------------------+
COMM | These are comments in the QUEST initialisation file. This file can   |
COMM | contain QUEST commands, such as terminal type, that are always read. |
COMM | For more information enter "HELP INITIALISATION FILES" within QUEST. |
COMM +----------------------------------------------------------------------+
COMM | For more information on...                                           |
COMM |    the database of CSDS citations,      type "HELP DBUSE"            |
COMM |    starting the graphical interface,    type "HELP GRAPHICS"         |
COMM |    the distributed release notes,       type "HELP RELEASE NOTES"    |
COMM |    the PreQuest data input program,     type "HELP PREQUEST"         |
COMM |    the CIF/MIF output file,             type "HELP SAVE"             |
COMM +----------------------------------------------------------------------+
COMM | Visit the CCDC web site at:             http://www.ccdc.cam.ac.uk/   |
COMM +----------------------------------------------------------------------+
COMM  Set better PRINT style:
      PRINT 10
COMM +----------------------------------------------------------------------+
SAVE 3
T1 *PCELL    TRICLINIC    4.001    7.730   16.760  90.05  94.08  90.05 0.010
QUESTION T1
---------+---------+---------+---------+---------+---------+---------+---------+
ZOSYEL01
2,3,5,6-Tetramethoxy-1,4-benzoquinone
C10 H12 O6
E.M.D.Keegstra,B.-H.Huisman,E.M.Paardekooper,F.J.Hoogesteger,J.W.Zwikker,L.W.Jen
      neskens,H.Kooijman,A.Schouten,N.Veldman,A.L.Spek
J.Chem.Soc.,Perkin Trans.2, , 229,1996
*RCP1=4.00100 // *RCP2=7.72999 // *RCP3=16.75995 // *RCP4=90.0000 // *RCP5=94.07
65 // *RCP6=90.0000 // *RCVO=517 //

[Platon CSD Cell Searching] | [Platon CSD Related Structure Searching] | [Platon - Generating CSD Quest Scripts for later use]
[Tutorials page] | [Platon Tutorial Index]
[Platon Introduction] | [Obtaining Platon] | [Installing and Running Platon] | [Starting out with Platon] | [Runthroughs of some Platon functionaltiy]
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