Présentation PowerPoint

Présentation PowerPoint

COD (CRYSTALLOGRAPHY
(CRYSTALLOGRAPHY OPEN
OPEN DATABASE)
DATABASE) and
and PCOD
PCOD (PREDICTED)
(PREDICTED)
COD
CODAdvisory
AdvisoryBoard
Board::
COD

DanielChateigner
Chateigner(France),
(France),XiaoLong
XiaoLongChen
Chen(China),
(China),Marco
MarcoE.
E.Ciriotti
Ciriotti(Italy),
(Italy),Lachlan
LachlanM.D.
M.D.Cranswick
Cranswick(Canada),
(Canada),
Daniel
RobertT.
T.Downs
Downs(USA),
(USA),Armel
ArmelLe
LeBail
Bail(France),
(France),Luca
LucaLutterotti
Lutterotti(Italy),
(Italy),Alexandre
AlexandreF.T.
F.T.Yokochi
Yokochi(USA)
(USA)
Robert
NewMembers
Members::Yoshitaka
YoshitakaMatsushita
Matsushita(Japan),
(Japan),Miguel
MiguelQuirs
QuirsOlozbal
Olozbal(Spain)
(Spain)
New

INTRODUCTION
INTRODUCTION
TheCOD
CODwas
wascreated
createdininMarch
March2003
2003and
andwas
wasbuilt
builton
onthe
the
The
PDBmodel
modelof
ofopen
openaccess
accesson
onthe
theInternet.
Internet.ItItisisintended
intended
PDB
thatthis
thisdatabase
database[1]
[1]consists
consistsof
ofany
anysmall
smallor
ormedium
medium
that
crystalstructure
structure(inorganic,
(inorganic,organic,
organic,organometallic).
organometallic).
crystal
Currentlythe
thetotal
totalentry
entrynumber
numberisisclose
closeto
to16000,
16000,including
including
Currently
6600entries
entriesfrom
fromthe
theAmerican
AmericanMineralogist
MineralogistCrystal
Crystal
6600
StructureDatabase
Database(AMCSD)
(AMCSD)[2],
[2],and
andCIF
CIFfiles
filesdonations
donations
Structure
fromaafew
fewlaboratories
laboratoriesininEurope
Europeor
orfrom
fromindividuals.
individuals.
from
Thedistribution
distributionisismade
madethrough
throughan
anApache/MYSQL/PHP
Apache/MYSQL/PHP
The
systemthat
thattakes
takesqueries
querieson
onchemistry,
chemistry,ranges
rangesof
ofcell
cell
system
parameters,volumes,
volumes,etc,
etc,as
aswell
wellas
ascombinations
combinationsof
offields,
fields,
parameters,
andcan
candownload
downloador
orupload
uploadCIF
CIFfiles.
files.
and

SEARCH the
the COD
COD
SEARCH
TheCOD
CODwishes
wishesto
tooffer
offerminimal
minimaland
andsimple
simplesearch
search
The
possibilities,allowing
allowingyou
you: :
possibilities,
toverify
verifyififthe
thestructure
structureyou
youintend
intendto
tosolve
solveisisnot
not
to
alreadysolved,
solved,
already
tofind
findmodels
modelsor
orfragments
fragmentsfor
forsolving
solvingyour
yourcurrent
current
to
problem,
problem,
tomake
makeaacorrect
correctjob
jobififan
aneditor
editorasks
asksyou
youto
to
to
reviewaamanuscript.
manuscript.
review

SEARCH OPTIONS
OPTIONS
SEARCH
Searchpage
page
Search

Results
Results

WHO NEEDS
NEEDS
WHO

??

OPEN DATA
DATA
OPEN

Petitiontext
textfor
forOpen
OpenData
Datain
inCrystallography:
Crystallography:
Petition
requestedthat
thatCSD,
CSD,ICSD,
ICSD,CRYSTMET
CRYSTMETand
andICDD
ICDD
ItItisisrequested
provideaalight
lightversion
versionof
oftheir
theircontent
content(crystal
(crystaldata
dataor
or
provide
powderpatterns)
patterns)at
atno
nocost
coston
onthe
theWeb.
Web.AAlight
lightversion
version
powder
consistsof
ofthe
thecomplete
completedatabase
databasethat
thatisisfully
fullysearchable
searchable
consists
onthe
theWeb
Webby
bycrystal
crystalparameters
parametersand
andreferences
referencesand
and
on
returnsthe
theCIFs.
CIFs.ItItwould
wouldnot
notconsist
consistof
ofthe
theother
other
returns
value-addedpossibilities
possibilitiesproduced
producedby
bythese
thesecompanies,
companies,
value-added
whichwould
wouldstay
stayinside
insideof
ofthe
thetoll
tollversions
versions- -unless,
unless,
which
ofcourse,
course,they
theywant
want to
togive
givemore...
more...The
Theprinciple
principle
of
defendedhere
hereisisthat
thatthe
theatomic
atomicpositions
positionsin
innatural
natural
defended
orsynthetic
syntheticcrystal
crystalsamples
samplesof
ofour
ourUniverse
Universe
or
arenot
notcopyrightable.
copyrightable.
are

and
and

CrystallographyDatabases
Databases
Crystallography

Openaccess
accesson
onthe
theWeb
Web::
Open
PDB(proteins)
(proteins)
PDB
NDB(nucleic
(nucleicacids)
acids)
NDB
AMCSD(minerals)
(minerals)
AMCSD

Tolldatabases
databases::
Toll

CSD(organic,
(organic,organometallic)
organometallic)
CSD
ICSD(inorganic,
(inorganic,minerals)
minerals)
ICSD
CRYSTMET(metals,
(metals,intermetallics)
intermetallics)
CRYSTMET
ICDD(powder
(powderpatterns)
patterns)
ICDD

PETITION RESULTS
RESULTS
PETITION
Between May and June 2005, included :

POSITION of
of ASSOCIATIONS
ASSOCIATIONS
POSITION

1150 YES signatures for the above text,
4 NO,
from 78 countries

Lettersfrom
fromthe
theCOD
CODto
to: :
Letters
IUCr(International
(InternationalUnion
Unionof
ofCrystallography),
Crystallography),
IUCr
ACS(American
(AmericanChemical
ChemicalSociety),
Society),
ACS
RSC(Royal
(RoyalSociety
Societyof
ofChemistry)
Chemistry)
RSC
askingthem
themfor
forthe
thepermission
permissionto
todownload
download
asking
systematicallythe
theCIF
CIFfiles
filesavailable
availableat
attheir
theirWeb
Websites,
sites,
systematically
havenot
notobtained
obtainedpositive
positiveanswer
answeryet.
yet.
have
Doletters
lettersfrom
frompetitioners
petitionerswill
willbe
bemore
moreconvincing
convincing??
Do

Including the signature of one Nobel
Laureate (Richard J. Roberts,
supporting PubChem as well)
35 countries with more than
5 signatures, representing
1054 signatures are listed on the
graph :
For understanding their motivations,
read the texts sent by the signers at:
http://www.crystallography.net/petition/
You can continue to sign (but not in
August due to a scheduled university
shutdown).

Karimat El-Sayed, Egypt:
Egypt is a developing country and we cannot have the regular
crystallographic databases which we really need in our work,
accordingly, if the crystallographic community allows us to have
it on line, it will be a big achievement for the third world countries.

DONATE your
your CIFs
CIFs
DONATE
Thepositions
positionsofofatoms
atomsininsamples
samples
The
ouruniverse
universe(natural
(naturalofofsynthetic)
synthetic)are
are
ofofour

NOTCOPYRIGHTABLE.
COPYRIGHTABLE.
NOT

uptotoyou
youtotosend
sendyour
yourCIFs
CIFstotothe
theCOD,
COD,
ItItisisup
youconsider
considerthat
thatthe
theaccess
accesstotothe
theKnowledge
Knowledge
ififyou
hastotobe
beopen
openfor
foracademic
academicresearch.
research.
has

GET the
the COD
COD TOOLS
TOOLS
GET
EasyPHP(Apache
(Apacheserver,
server,MySQL,
MySQL,PHP
PHPscripts)
scripts)
EasyPHP
Youcan
candownload
downloadthe
thecomplete
completedatabase
databaseand
andmake
makeititrun
runon
onyour
yourPC.
PC.
You
Youcan
canreuse
reusethe
thecomplete
completesystem
systemand
andcreate
createyour
yourlab
labCIF
CIFrepository.
repository.
You

A crystallography program
like MAUD can send
directly CIFs to the COD :
Why not to modify your
own computer program as
well (SHELX, SIR, Rietveld,
etc) in order to send
automatically the final CIF
to the COD through the
Internet ?

PCOD
PCOD
ThePCOD,
PCOD,created
createdin
inDecember
December2003,
2003,isisaaCOD
CODsubset
subsetof
of
The
crystalstructures
structurespredicted
predictedby
bythe
theGRINSP
GRINSPcomputer
computer
crystal
program[3]
[3]. .ItItisisgrowing
growingfast
fastand
andalready
alreadycontains
contains>>1500
1500
program
CIFfiles
filescorresponding
correspondingto
toMMX
X , MX , M2X,5,MX
MX3or
orMMM
MbXc
CIF
2 2 3,3 MX2,2 M2X
5
3
a a bX
c
formulations(X
(X==O,
O,F;
F;M/M
M/M==B,
B,Na,
Na,Si,
Si,Al,
Al,P,
P,Ca,
Ca,V,
V,Fe,
Fe,Re,
Re,
formulations
Zr,etc),
etc),including
includinghypothetical
hypotheticalzeolites
zeolitesand
andother
otherbinary
binary
Zr,
compoundswith
withN-connected
N-connected3D
3Dframeworks
frameworksof
ofMMatoms
atoms
compounds
(N==3,3,4,4,5,5,6)
6)as
aswell
wellas
asternary
ternarycompounds
compoundswith
withmixed
mixed
(N
M/Mframeworks.
frameworks.The
ThePCOD
PCODisisopen
openfor
forsearch,
search,download
download
M/M
andupload
uploadof
ofpredicted
predictedcrystal
crystalstructures
structures(coming
(comingfrom
fromany
any
and
predictioncomputer
computerprogram,
program,inorganic
inorganicor
orsmall
smalland
and
prediction
mediumorganic
organicmolecules).
molecules).
medium

DONATORS/SPONSORS
DONATORS/SPONSORS

SEARCHING PCOD
PCOD
SEARCHING
Searchpage
page
Search

Results
Results

Zeolite
Zeolite

CONCLUSION
CONCLUSION
(IUCrasked
askedtotothe
theCOD
CODtotoobtain
obtainletters
lettersfrom
frompeople
peopleinterested)
interested)
(IUCr

http://www.crystallography.net/petition/
http://www.crystallography.net/petition/

CRISMAT

Thanksto
tothem
themand
andto
toindividuals
individualssending
sendingCIFs
CIFs! !
Thanks

nanotubes
BB2O
2O
3 3nanotubes

[Ca3Al4F21]3-

Continueto
tosign
signthe
thepetition
petition
Continue

Laboratories: :
Laboratories

VIRTUAL MODELS
MODELS in
in PCOD
PCOD
VIRTUAL

Waitingfor
foran
animprobable
improbablepositive
positiveanswer
answer
Waiting
fromCSD,
CSD,ICSD,
ICSD,CRYSTMET,
CRYSTMET,ICDD,
ICDD,
from
continueto
tosend
sendyour
yourCIFs
CIFsto
tothe
theCOD
COD(and
(andPCOD)
PCOD)
continue
http://www.crystallography.net/
http://www.crystallography.net/

THANKYOU
YOU!!
THANK

REFERENCES
REFERENCES
[1]http://www.crystallography.net/
http://www.crystallography.net/
[1]
[2]http://www.geo.arizona.edu/AMS/amcsd.php
http://www.geo.arizona.edu/AMS/amcsd.php
[2]
[3]http://www.cristal.org/grinsp/
http://www.cristal.org/grinsp/
[3]
Emails
Emails
COD/PCOD: :[email protected]
[email protected]
COD/PCOD

D.Chateigner
Chateigner: :[email protected]
[email protected]
D.
X.L.Chen
Chen: :[email protected]
[email protected]
X.L.
M.E.E.Ciriotti
Ciriotti: :[email protected]
[email protected]
M.
L.M.D.Cranswick
Cranswick: :[email protected]
[email protected]
L.M.D.
R.T.T.Downs
Downs: :[email protected]
[email protected]
R.
A.Le
LeBail
Bail: :[email protected]
[email protected]
A.
Lutterotti: :[email protected]
[email protected]
L.L.Lutterotti
A.F.T.Yokochi
Yokochi: :[email protected]
[email protected]
A.F.T.

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