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Tutorials and Examples

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

Creating a CSD (Cambridge Structure Database) Quest Query of an organic or organometallic stucture using Platon

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 is the ability to create a CSD Quest database query of the structure for checking if the structure you have refined has already been published or submitted to the Cambridge database and also check what related published phases are in the database. It is of course quite excellent for using when a referee of organic and organimetallic structures relevant to the Cambridge Database.


For directly interacting with the CSD database on a separate UNIX server from a MS-Windows computer, the following links to information on settup up for Secure FTP and Secure X sessions from a Windows machine:


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 an organic phase taken from Marcus Bonds web site of example structures.

Open the Structure of interest (in this case title ladd5c).

Main menu of Platon

This is a view of the structure that is being checked with CSD Quest.

LADD5c Structure being viewed in
Platon


Under the REPORT option, select CSD-QUEST and Platon will generate the Quest file. If on a UNIX machine running Quest, Platon will automatically spawn quest and pass it the file. The following screen dumps were created on a Windows Machine so they will have to be passed manually to the UNIX computer running Quest (this is why Platon is stating at the bottom in red that the "Requested Program not Accessible"). A QUE file will be created with the CSD Quest query.

After a CSD QUEST query file has
been generated


Copy the QUE file to a machine with CSD Quest. RUN quest and import the file.

quest -j structure_name < structure_name.que

Click here to see the ladd5c.que CSD QUEST Query file

QUESTION T1
---------+---------+---------+---------+---------+
YOMTAV
bis((mu!2$-Diphenylphosphonato-O,O')-(hydrogen 
tris(3,5-dimethylpyrazolyl)borato)-oxo-vanadium) toluene solvate
C54 H64 B2 N12 O10 P2 V2,C7 H8
M.R.Bond,L.M.Mokry,T.Otieno,J.Thompson,C.J.Carrano
Inorg.Chem., 34, 1894,1995

In this case, there are no related structures so we have only found out that it has been solved.


Click here to see the ladd5c Journal result file from CSD Quest which shows that this structure has already been published, thus saving you the embaressment of submitting this to a journal and having it turfed back in your face for not being an original structure solution.

Click here to see the YOMTAV Structure data from the CSD database.

This can be directly viewed in Platon or other programs such as Ortep-3.

YOMTAV Structure being Viewed in GUIWinORTEP


[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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If you have any queries or comments, please feel free to contact the CCP14