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Tutorials and Examples

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

CSD (Cambridge Structure Database) Structure searching - Using Platon as a user-friendly interface into Quest to check for published and related structures for a locally solved structure

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.

In the following case, we will give Platon the structure 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.

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)


Following is the solved and refined structure information (and available as a downloadable sdemo.res 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 filename.res (or ins, spf or CIF file). 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.

Following is how the structure looks in Platon using Pluton, then ADP (ORTEP) mode. (Just use the options under Graphics to do this.

Viewing the structure in Pluton mode

Viewing the structure in APD/ORTEP mode


Under the REPORT option, select CSD-QUEST 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 finding hits!

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

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

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 Quest 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 *CONNSER
AT1  O     2
AT2  O     2
AT3  O     1
AT4  C     3
AT5  C     3
AT6  C     3
AT7  C     1
AT8  C     1
AT9  O     2
AT10  O     2
AT11  O     1
AT12  C     3
AT13  C     3
AT14  C     3
AT15  C     1
AT16  C     1
BO     1     4 99
BO     1     8 99
BO     2     5 99
BO     2     7 99
BO     3     6 99
BO     4     5 99
BO     4     6 99
BO     5    14 99
BO     6    13 99
BO     9    12 99
BO     9    16 99
BO    10    13 99
BO    10    15 99
BO    11    14 99
BO    12    13 99
BO    12    14 99
END
QUESTION T1


A portion of the Resulting Journal File
---------+---------+---------+---------+---------+---------+---------+---------+
AXMAIN
(+-)-2-Acetoxymethyl-1,3,4,6-tetra-O-acetyl-epi-inositol
C17 H24 O12
H.Sternglanz,C.E.Bugg
Acta Crystallogr.,Sect.B, 29, 1536,1973
---------+---------+---------+---------+---------+---------+---------+---------+
CAKGOK
hexakis(Phenyloxy)-benzene
C42 H30 O6
C.J.Gilmore,D.D.MacNicol,A.Murphy,M.A.Russell
Tetrahedron Lett., 24, 3269,1983
---------+---------+---------+---------+---------+---------+---------+---------+
CAKGUQ
hexakis(3,5-Dimethylphenyloxy)-benzene acetonitrile clathrate
C54 H54 O6,C2 H3 N1
C.J.Gilmore,D.D.MacNicol,A.Murphy,M.A.Russell
Tetrahedron Lett., 24, 3269,1983
---------+---------+---------+---------+---------+---------+---------+---------+
FENMAM
1-O-Camphanoyl-2,3,4,5,6-penta-O-benzyl-myo-inositol
C51 H54 O9
D.C.Billington,R.Baker,J.J.Kulagowski,I.M.Mawer
Chemical Communications, , 314,1987
---------+---------+---------+---------+---------+---------+---------+---------+
FOPHEX
hexakis(p-Hydroxyphenyloxy)benzene hexapyridine monohydrate clathrate
6(C5 H5 N1),C42 H30 O12,x(H2 O1)
D.D.MacNicol,P.R.Mallinson,A.Murphy,C.D.Robertson
J.Inclusion Phenom., 5, 233,1987
---------+---------+---------+---------+---------+---------+---------+---------+
GLINST
2-((5-Bromo-2,4-dinitrophenyl)-amino)-2-deoxy-alpha-D-glucopyranosyl-1-O-D-myo-i
      nositol octa-acetate
C34 H40 Br1 N3 O22
H.Maehr,J.M.Smallheer,J.F.Blount
J.Org.Chem., 46, 378,1981
---------+---------+---------+---------+---------+---------+---------+---------+
HADKIG
rac-3,4-Di-O-acetyl-1,2,5,6-tetra-O-benzyl-myo-inositol
form 1
C38 H40 O8
T.Steiner,W.Hinrichs,W.Saenger,R.Gigg
Acta Crystallogr.,Sect.B (Str.Sci.), 49, 708,1993
---------+---------+---------+---------+---------+---------+---------+---------+
HADKIG01
rac-3,4-Di-O-acetyl-1,2,5,6-tetra-O-benzyl-myo-inositol
form 2
C38 H40 O8
T.Steiner,W.Hinrichs,W.Saenger,R.Gigg
Acta Crystallogr.,Sect.B (Str.Sci.), 49, 708,1993
---------+---------+---------+---------+---------+---------+---------+---------+
HADKIG02
rac-3,4-Di-O-acetyl-1,2,5,6-tetra-O-benzyl-myo-inositol
form 2, at 60 deg.C
C38 H40 O8
T.Steiner,W.Hinrichs,W.Saenger,R.Gigg
Acta Crystallogr.,Sect.B (Str.Sci.), 49, 708,1993
---------+---------+---------+---------+---------+---------+---------+---------+
HADKIG03
rac-3,4-Di-O-acetyl-1,2,5,6-tetra-O-benzyl-myo-inositol
form 3, at 80 deg.C
C38 H40 O8
T.Steiner,W.Hinrichs,W.Saenger,R.Gigg
Acta Crystallogr.,Sect.B (Str.Sci.), 49, 708,1993
---------+---------+---------+---------+---------+---------+---------+---------+
KAHXOG
hexakis(eta$6!-hexakis(p-Methoxyphenoxy)benzene)-hexakis(eta$5!-pentamethyl-cycl
      opentadienyl)-hexa-ruthenium hexakis(trifluoromethanesulfonate) nitrometha
      ne solvate
at -70 deg.C
C108 H132 O12 Ru6 6+,6(C1 F3 O3 S1 1-),6(C1 H3 N1 O2)
P.J.Fagan,M.D.Ward,J.C.Calabrese
J.Am.Chem.Soc., 111, 1698,1989
---------+---------+---------+---------+---------+---------+---------+---------+
KOVDAA
syn-4,6,8,10,42,44,46,48-Octapentyl-2,12:3,11:40,50:41,49-tetrametheno-4H,6H,8H,
      10H,42H,44H,46H,48H-bis(1,3)dioxocino(5'',4'':8',9')(1,3)benzodioxocino(5'
       4':8,9)(1,3)benzodioxocino(5,4-j:5',4'-j')benzo(1,2-b:5,4-b')bis(1,4)benz
      odioxonin-26,52-dione acetonitrile chloroform clathrate
C108 H124 O18,3(C2 H3 N1),C1 H2 Cl2
D.J.Cram,L.M.Tunstad,C.B.Knobler
J.Org.Chem., 57, 528,1992
---------+---------+---------+---------+---------+---------+---------+---------+
KOVDEE
anti-4,6,8,10,42,44,46,48-Octapentyl-2,12:3,11:40,50:41,49-tetrametheno-4H,6H,8H
      ,10H,42H,44H,46H,48H-bis(1,3)dioxocino(5'',4'':8',9')(1,3)benzodioxocino(5
      ' 4':8,9)(1,3)benzodioxocino(5,4-j:5',4'-j')benzo(1,2-b:5,4-b')bis(1,4)ben
      zodioxonin-26,52-dione tetrakis(ethyl methyl ketone) clathrate
C108 H124 O18,4(C4 H8 O1)
D.J.Cram,L.M.Tunstad,C.B.Knobler
J.Org.Chem., 57, 528,1992
---------+---------+---------+---------+---------+---------+---------+---------+
KOVDII
anti-4,6,8,10,42,44,46,48-Octapentyl-2,12:3,11:40,50:41,49-tetrametheno-4H,6H,8H
      ,10H,42H,44H,46H,48H-bis(1,3)dioxocino(5'',4'':8',9')(1,3)benzodioxocino(5
      ' 4':8,9)(1,3)benzodioxocino(5,4-j:5',4'-j')benzo(1,2-b:5,4-b')bis(1,4)ben
      zodioxonin-26,52-dione tetrakis(ethyl acetate) clathrate
C108 H124 O18,4(C4 H8 O2)
D.J.Cram,L.M.Tunstad,C.B.Knobler
J.Org.Chem., 57, 528,1992
---------+---------+---------+---------+---------+---------+---------+---------+
KOVDOO
anti-4,6,8,10,42,44,46,48-Octapentyl-2,12:3,11:40,50:41,49-tetrametheno-4H,6H,8H
      ,10H,42H,44H,46H,48H-bis(1,3)dioxocino(5'',4'':8',9')(1,3)benzodioxocino(5
      ',4':8,9)(1,3)benzodioxocino(5,4-j:5',4'-j')benzo(1,2-b:5,4-b')bis(1,4)ben
      zodioxonin-26,52-dione nitrobenzene clathrate
C108 H124 O18,6(C6 H5 N1 O2)
D.J.Cram,L.M.Tunstad,C.B.Knobler
J.Org.Chem., 57, 528,1992
---------+---------+---------+---------+---------+---------+---------+---------+
NEJDOV
meso-5,10,15,20-tetrakis(2-Hydroxy-1-naphthyl)porphyrin tetramethoxy-p-benzoquin
      one chloroform solvate
1.5(C60 H38 N4 O4),1.5(C10 H12 O6),2(C1 H1 Cl3)
T.Hayashi,T.Miyahara,N.Koide,Y.Kato,H.Masuda,H.Ogoshi
J.Am.Chem.Soc., 119, 7281,1997
---------+---------+---------+---------+---------+---------+---------+---------+
NODDIT
endo-4,6-O-Benzylidene-exo-3,5-ethylidene-1,2-di-O-methyl-myo-inositol
C17 H22 O6
Sue-Min Yeh,Gene Hsiang Lee,Yu Wang,Tien-Yau Luh
J.Org.Chem., 62, 8315,1997
---------+---------+---------+---------+---------+---------+---------+---------+
RONHEH
Hexa-O-methyl-epi-inositol
C12 H24 O6
J.E.Anderson,S.J.Angyal,D.C.Craig
J.Chem.Soc.,Perkin Trans.2, , 729,1997
---------+---------+---------+---------+---------+---------+---------+---------+
TAFQUM
1,7,12,17,22-Pentaoxapentaspiro(4.0.4.0.4.0.4.0.4.1)hexacosan-26-ol
at -150 deg.C.
C21 H32 O6
L.A.Paquette,M.Stepanian,B.M.Branan,S.D.Edmondson,C.B.Bauer,R.D.Rogers
J.Am.Chem.Soc., 118, 4504,1996
---------+---------+---------+---------+---------+---------+---------+---------+
TAFQUM10
Cyclohexanol-2,3,4,5,6-pentaspiro-(tetrahydrofuran)-5-yl
at -150 deg.C.
C21 H32 O6
L.A.Paquette,B.M.Branan,M.Stepanian
Tetrahedron Lett., 37, 1721,1996
---------+---------+---------+---------+---------+---------+---------+---------+
TAFSIC
1,7,12,17,22,27-Hexaoxahexaspiro(4.0.4.0.4.0.4.0.4.0.4.0)triacontane
at 173 deg.K
C24 H36 O6
L.A.Paquette,M.Stepanian,B.M.Branan,S.D.Edmondson,C.B.Bauer,R.D.Rogers
J.Am.Chem.Soc., 118, 4504,1996
---------+---------+---------+---------+---------+---------+---------+---------+
TEKPUU
(+-)-cis-1,2-O-Cyclohexylidene-3,4,5,6-tetra-O-benzyl-myo-inositol
C40 H44 O6
I.D.Spiers,C.H.Schwalbe,S.Freeman
Acta Crystallogr.,Sect.C (Cr.Str.Comm.), 52, 2575,1996
---------+---------+---------+---------+---------+---------+---------+---------+
TERCIC
1D-1-O-Allyl-3,6-di-O-benzyl-2-O((-)-camphanoyl)-4,5-O-isopropylidene-scyllo-ino
      sitol
C36 H44 O9
D.Lampe,Changsheng Liu,M.F.Mahon,B.V.L.Potter
J.Chem.Soc.,Perkin Trans.1, , 1717,1996
---------+---------+---------+---------+---------+---------+---------+---------+
VEXRAR
1,2,3,4,5,6-Hexa-O-acetyl-myo-inositol
at 163 deg.K,possible physiological activity
C18 H24 O12
K.A.Abboud,S.H.Simonsen,R.J.Voll,E.S.Younathan
Acta Crystallogr.,Sect.C (Cr.Str.Comm.), 46, 2208,1990
---------+---------+---------+---------+---------+---------+---------+---------+
WAJJIA
hexakis(4-(2-Phenylpropan-2-yl)phenoxy)benzene
C96 H90 O6
D.D.MacNicol,P.R.Mallinson,I.Vallance
J.Phys.Org.Chem., 5, 628,1992
---------+---------+---------+---------+---------+---------+---------+---------+
YADDEM
hexakis(p-Phenoxyphenoxy)benzene methyl iodide clathrate
C78 H54 O12,C1 H3 I1
A.A.Freer,D.D.MacNicol,P.R.Mallinson,I.Vallance
Tetrahedron Lett., 33, 261,1992
---------+---------+---------+---------+---------+---------+---------+---------+
YADDOW
hexakis(p-Phenoxyphenoxy)benzene carbonyl dichloride clathrate
C78 H54 O12,C1 Cl2 O1
A.A.Freer,D.D.MacNicol,P.R.Mallinson,I.Vallance
Tetrahedron Lett., 33, 261,1992
---------+---------+---------+---------+---------+---------+---------+---------+
YADDOX
hexakis(p-Benzylphenoxy)benzene 1,1,1-trichloroethane clathrate
C84 H66 O6,C2 H3 Cl3
A.A.Freer,D.D.MacNicol,P.R.Mallinson
Tetrahedron Lett., 33, 261,1992
---------+---------+---------+---------+---------+---------+---------+---------+
ZOKGEL
ZOKGEL
1,4-Diacetoxy-tetramethoxybenzene
C14 H18 O8
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
---------+---------+---------+---------+---------+---------+---------+---------+
ZOKGIP
1,4-Diacetoxy-tetradecyloxybenzene
C50 H90 O8
E.D.Keegstra,B.-H.Huisman,E.M.Paardekooper,F.J.Hoogesteger,J.W.Zwikker,L.W.Jenne
      skens,H.Kooijman,A.Schouten,N.Veldman,A.L.Spek
J.Chem.Soc.,Perkin Trans.2, , 229,1996
---------+---------+---------+---------+---------+---------+---------+---------+
ZOSSEF
Hexa-O-methyl-scyllo-inositol
C12 H24 O6
J.E.Anderson,S.J.Angyal,D.C.Craig
Carbohydr.Res., 272, 141,1995
---------+---------+---------+---------+---------+---------+---------+---------+
ZOSYEL
Tetramethoxy-p-benzoquinone
C10 H12 O6
H.Bock,S.Nick,W.Seitz,C.Nather,J.W.Bats
Z.Naturforsch.,Teil B, 51, 153,1996


[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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