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Methods, Problems and Solutions

Powder Diffraction Structure Solution Pathways

Solving an Organic Structure (Cimetidine - C 10 H 16 N6 S) from Powder Diffraction Data

CELL Searching the Cambridge database via Platon and Quest

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]

[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]

[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

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)

TITL Cimetidine
CELL  1.52904  10.392     18.815     6.823      90.00     106.44    90.00   
ZERR  4         0.0030     0.0030    0.0030      0.0000     0.0500   0.0000         
SFAC C  H  N S
UNIT 10 16 6 1
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 cime.ins. This will spawn the following window in your windows X-server.

Running a UNIX Platon via a 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.

Setting the CELL search tolerance in Platon to 0.05


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 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!

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.


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   10.392   18.815    6.823  90.00 106.44  90.00 0.050
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   10.392   18.815    6.823  90.00 106.44  90.00 0.050
QUESTION T1
---------+---------+---------+---------+---------+---------+---------+---------+
CIMETD
N''-Cyano-N-methyl-N'-(2-((5-methyl-1H-imidazol-4-yl)-methylthio)-ethyl)-guanidi
      ne
Cimetidine
monoclinic form A, histamine H2-receptor antagonist activity
C10 H16 N6 S1
E.Hadicke,F.Frickel,A.Franke
Chem.Ber., 111, 3222,1978
*RCP1=6.82099 // *RCP2=10.37399 // *RCP3=18.81797 // *RCP4=90.0000 // *RCP5=90.0
000 // *RCP6=106.4199 // *RCVO=1277 //
---------+---------+---------+---------+---------+---------+---------+---------+
CIMETD02
Cimetidine
N''-Cyano-N'-methyl-N-(2-((5-methyl-1H-imidazol-4-yl)methylthio)ethyl)guanidine
powerful histamine antagonistic activity
C10 H16 N6 S1
S.R.Critchley
Private Communication, , ,1979
*RCP1=6.81599 // *RCP2=10.38736 // *RCP3=18.81297 // *RCP4=90.0000 // *RCP5=90.0
000 // *RCP6=106.3878 // *RCVO=1278 //
---------+---------+---------+---------+---------+---------+---------+---------+
CIMETD03
Cimetidine
N''-Cyano-N'-methyl-N-(2-((5-methyl-1H-imidazol-4-yl)methylthio)ethyl)guanidine
powerful histamine antagonistic activity
C10 H16 N6 S1
R.J.Cernik,A.K.Cheetham,C.K.Prout,D.J.Watkin,A.P.Wilkinson,B.T.M.Willis
J.Appl.Crystallogr., 24, 222,1991
*RCP1=6.82659 // *RCP2=10.39513 // *RCP3=18.82617 // *RCP4=90.0000 // *RCP5=90.0
000 // *RCP6=106.4157 // *RCVO=1282 //
---------+---------+---------+---------+---------+---------+---------+---------+
ZORHOD
1,2,3-Trimethyl-5,5,9-trinitrotetracyclo(4.2.1.1.0)-6,7,10-azadioxadec-2-ene
at 130 deg.K
C10 H12 N4 O8
C.P.Butts,L.Eberson,M.P.Hartshorn,W.T.Robinson,D.J.Timmerman-Vaughan,D.A.W.Young

Acta Chem.Scand., 50, 29,1996
*RCP1=6.81200 // *RCP2=10.44000 // *RCP3=18.84400 // *RCP4=101.1700 // *RCP5=90.
0000 // *RCP6=90.0000 // *RCVO=1315 //


[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]

[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]

[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

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