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CSD Quick ver.1.1 2013.1.25
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113-0021
6-25-4
TEL03-5978-3622 FAX03-5978-3600
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CSD Quick
1.
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2
2. .............................................................
3
2.1. ConQuest
..............................................................
3
2.2.
..................................................................................
4
2.3.
......................................................................................
7
3. ..................................................... 11
3.1. Mercury
........................................................ 11
3.2.
................................................................................
12
3.3. ............................. 13
4.
.................................................................................
16
4.1. Mogul .... 16
4.2. ......................................................
18
4.3. MercuryData Analysis....... 20
4.4. IsoStar ............................. 26
5. In-house
....................................................................
30
5.1. PreQuest ConQuest
............................................. 30
5.2. ConQuest
.........................................................................
31
5.3. in-house ............................... 31
1. CSD 2012 Release
2. ConQuestMercuryMogulIsoStarHelp Tutorials
3. CSD
4. CCDC website
CCDCSupport & ResourcesSupport
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2
1.
1.1.
Quick Install GuideInstallation Help
()
ConQuest
Mercury
Solid Form module ()
Mogul
PreQuestin-house CSD library format
IsoStar CCDC in-house
Documentation
IsoStar
1.2.
ConQuest
Site Number ()Confirm Code()(
CSD)
EnglishVisual C run time
Site Number Confirm Code
Online
Browse Video Help
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3
2.
2.1. ConQuest
ConQuest
Draw
Peptide
Author/Journal
CCDC No.
Name/Class
Formula()1
Space Group
Unit Cell
Reduced cell
Z/Density(g/cm3)
ExperimentalR C-C
e.s.d X
Text(green, yellow )
(explosive, drug)
Refcode(entry ID)CSD
query
2
2
Build Queries
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4
2.2.
2.2.1. Draw
2.2.2.
CAtoms/Hydrogens
/Generate/All Atoms
DRAW
EDIT
Delete
ERASE
ADD 3D
CONTACT
RingMaker
Ctrl+Z
Atoms/Hydrogens/Generate/All atoms
AnyMore
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5
()
Search
Search SetupFilters Advanced Options
Start Search
Stop Search
Build Queries
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6
2.2.3.
116
3
BPPFBP
Use as Query
Build Queries
Filters
Edit
Combine Queries Query
Manage Hitlists
2 2
Mercury Analyse
HitlistVisualise structures
Mercury Export
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7
2.2.4.
File/Export Entries as
cif
File/Export entries as
cifMercuryQuery
File/Save Search as.
2.3.
2.3.1.
ConQuest
2
1. N 3
2. OH 0 - 2.1
3. ON
DRAW
export
export
All selected entries
export
export
0 2.1
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8
2.3.2. 1 N
N3NNumber of Bonded Atoms/3
NT3
2.3.3. 2 OH
OHCONTACT
2DefineEdit
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9
OHO H
0 - 2.1Inter-molecular
Distance rangeOKDone
2.3.4. 3 O N
DRAWADD 3D O N
ON(non-bonded interaction)ADD 3D
ONDistanceDefine
ContactOKDefineOK
DoneO N
OH-NC-OH
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10
2.3.5.
SearchStart Search
3D VisualiserOH
Analyse Hitlist
Visualise Structure
Mercury
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11
3.
3.1. Mercury
cifMercuryFile/Open
Window()
(
Short Contact
)
(
H-Bond)
CSD
Refcode
View/Tools
File/Save as
format
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12
3.2.
CSDMercury(Mercury
)1 Multiple
Structures
File/Open
Structures
2
1
2
CSD Mercury
Multiple StructuresStructure
Navigator
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13
1 2
Calculate/Structure Overlay
3.3.
3.3.1.
2 carbamoyl (
)MercurySolid Form/Motifs
Select pre-defined motif(s)
Create new motifsNext
Add
1
2
Solid Form module
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14
carbamoylOKNext
Add
3.3.2.
carbamoylNOOK
Next
3.3.3.
Next
33Next
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15
CSDSelect
Next
Search NameStart Search
3.3.4.
CSD
(Carbamoyl
)
ConQuest 3D
Solid Form module
Propensity Prediction
Tool
33
+
Filter
Option
Filter Results
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16
4.
4.1. Mogul
4.1.1.
Mogul
CSD
(cif, mol2
) 4
Calculate/Mogul Geometry Check
4.1.2.
Filter Search()
Picking Mode Select Atoms
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17
4.1.3.
(enough hits)
() torsion
4.1.4.
CSD
30 150
Deselect
(
Torsion Angles)
Filter
()
(Query value) 145.310Not unusual
( 145)
Filter
CSD
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18
Deselect
145150
View Structures
Mogul
(C H)()
N Mogul
Filter
4.2.
4.2.1. Mogul
4.1(3D)Mogul CSD
2D Mogul
MogulDRAW
596 543
Torsion angle
147.486 3D
596/10,000
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19
DrawConQuest
DrawDone
.
Search
All fragments
Filter
(3D)Load cif, mol, res
(2D )
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20
4.2.2.
4.1.3.
4.3. MercuryData Analysis
4.3.1.
ConQuest
Mercury C-C-S-N
ConQuestDRAW
4.3.2
ADD 3D
CSD Mercury
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21
C1-C6-S-N Torsion
DefineTOR1Done
TOR1 0-3600 180
Options
APPLY FUNCTION AbsoluteApply,Close
Search
Start Search
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4.3.3.
Analyse Hitlist
Analyse Data
4.3.4. Mercury
Analyse in Mercury
Mercury
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23
4.3.5.
Plot/HistogramHistogram
TOR1OK
/Configure
Display/Configure
Number of bins90
Axis rangesY040ApplyOK
20
0-180 20
X 9
2
90
X,Y 2
Y
40
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4.3.6.
MercuryStructure Navigation
(
BAGVUA)
109.11
108-110
Ctrl
Picking mode: Measure Torsion
BAGVUA
Structure Navigator
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4.1.3Mogul
4.3.6.
1ConQuest
(ConQuest)
4.3.7.
()Selection/Filter
TOR1OK
gray out
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4.3.8. export
Data Analysis CSD
Data Analysis
Spread sheet export
Tools/CSD data
R-factorradiation sourceOK
R-factorradiation source
File/Export csv export
4.4. IsoStar
4.4.1. IsoStar
IsoStarCSD PDB
IsoStarCCDC Support & Resources
DocumentationIsoStarInstallation Notes IsoStar serverCCDC
Linux
Mercury
Help file/Tutorials
http://beta-www.ccdc.cam.ac.uk/Lists/DocumentationList/release_install_notes.pdf
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4.4.2.
()Mercury
(Refcode: DECFDP01)
FCalculate/IsoStar Intermolecular Contact
DatabaseOK
IsoStar
IsoStar
CSD( 933)OK
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4.4.3.
Scatter plot
Create/Edit
new surface(s) using ProbecarbonCreate
(Contour density surface)
(Scatter plot)
Expand
Contact
carbon
vdW
(crush)
( vdW
) - 0.91( vdW
) + 0.5
Scatter plot
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4.4.4.
IsoStar
Level
CSD()Hyperlink
Hide All Central group Contour
density surface
IsoStar Help file
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5. In-house
CSD in-house ConQuest
PreQuest(ConQuestMercury
)
5.1. PreQuest ConQuest
1. ConQuestcif res
2. PreQuest
3. ConQuest
Preferences Relaxed (minimal
rules)CCDC Strict (full CCDC rules)
4. Reference
warning(
)
5. Export. ASER (File Format)
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5.2. ConQuest
1. 5.1 .msk, .tcd, .ind CSD
(C:Program FilesCCDCCSD V5.33)
2. ConQuest in-house database
CCDCCSDActive In-house database
3. Active Exit
5.3. in-house
1. PreQuest.ind
2. 1D Edit Refcode(ABUBUV)
?DELETEME ABUBUV
3. Refcode ABUBUV
YesContinue
4. format export
5.1.
