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1U8R
Asym. Unit
Info
Asym.Unit (345 KB)
Biol.Unit 1 (171 KB)
Biol.Unit 2 (170 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AN IDER-DNA COMPLEX REVEALS A CONFORMATIONAL CHANGE IN ACTIVATED IDER FOR BASE-SPECIFIC INTERACTIONS
Authors
:
G. Wisedchaisri, R. K. Holmes, W. G. J. Hol
Date
:
06 Aug 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Ider, Iron-Dependent Regulator, Iron Acquisition, Siderophores, Mycobacterium Tuberculosis, Metal-Binding Protein, Transcription/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Wisedchaisri, R. K. Holmes, W. G. J. Hol
Crystal Structure Of An Ider-Dna Complex Reveals A Conformational Change In Activated Ider For Base-Specific Interactions.
J. Mol. Biol. V. 342 1155 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 32)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
1e: COBALT (II) ION (COe)
1f: COBALT (II) ION (COf)
1g: COBALT (II) ION (COg)
1h: COBALT (II) ION (COh)
1i: COBALT (II) ION (COi)
1j: COBALT (II) ION (COj)
1k: COBALT (II) ION (COk)
1l: COBALT (II) ION (COl)
1m: COBALT (II) ION (COm)
1n: COBALT (II) ION (COn)
1o: COBALT (II) ION (COo)
1p: COBALT (II) ION (COp)
1q: COBALT (II) ION (COq)
1r: COBALT (II) ION (COr)
1s: COBALT (II) ION (COs)
1t: COBALT (II) ION (COt)
1u: COBALT (II) ION (COu)
1v: COBALT (II) ION (COv)
1w: COBALT (II) ION (COw)
1x: COBALT (II) ION (COx)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
2e: SODIUM ION (NAe)
2f: SODIUM ION (NAf)
2g: SODIUM ION (NAg)
2h: SODIUM ION (NAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
24
Ligand/Ion
COBALT (II) ION
2
NA
8
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(32, 32)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:79 , GLU A:83 , HIS A:98 , GLU A:172 , GLN A:175
BINDING SITE FOR RESIDUE CO A 1001
02
AC2
SOFTWARE
MET A:10 , CYS A:102 , GLU A:105 , HIS A:106
BINDING SITE FOR RESIDUE CO A 1002
03
AC3
SOFTWARE
HIS A:219 , HIS A:223
BINDING SITE FOR RESIDUE CO A 1003
04
AC4
SOFTWARE
HIS B:79 , GLU B:83 , HIS B:98 , GLU B:172 , GLN B:175
BINDING SITE FOR RESIDUE CO B 2001
05
AC5
SOFTWARE
MET B:10 , CYS B:102 , GLU B:105 , HIS B:106
BINDING SITE FOR RESIDUE CO B 2002
06
AC6
SOFTWARE
HIS B:219 , HIS B:223 , HOH B:2105
BINDING SITE FOR RESIDUE CO B 2003
07
AC7
SOFTWARE
HIS C:79 , GLU C:83 , HIS C:98 , GLU C:172 , GLN C:175
BINDING SITE FOR RESIDUE CO C 3001
08
AC8
SOFTWARE
MET C:10 , CYS C:102 , GLU C:105 , HIS C:106
BINDING SITE FOR RESIDUE CO C 3002
09
AC9
SOFTWARE
HIS C:219 , HIS C:223 , HOH C:3107 , HOH C:3109
BINDING SITE FOR RESIDUE CO C 3003
10
BC1
SOFTWARE
HIS D:79 , GLU D:83 , HIS D:98 , GLU D:172 , GLN D:175
BINDING SITE FOR RESIDUE CO D 4001
11
BC2
SOFTWARE
MET D:10 , CYS D:102 , GLU D:105 , HIS D:106
BINDING SITE FOR RESIDUE CO D 4002
12
BC3
SOFTWARE
HIS D:219 , HIS D:223 , HOH D:4107
BINDING SITE FOR RESIDUE CO D 4003
13
BC4
SOFTWARE
HIS G:79 , GLU G:83 , HIS G:98 , GLU G:172 , GLN G:175
BINDING SITE FOR RESIDUE CO G 5001
14
BC5
SOFTWARE
MET G:10 , CYS G:102 , GLU G:105 , HIS G:106
BINDING SITE FOR RESIDUE CO G 5002
15
BC6
SOFTWARE
HIS G:219 , HIS G:223 , HOH G:5107
BINDING SITE FOR RESIDUE CO G 5003
16
BC7
SOFTWARE
HIS H:79 , GLU H:83 , HIS H:98 , GLU H:172 , GLN H:175
BINDING SITE FOR RESIDUE CO H 6001
17
BC8
SOFTWARE
MET H:10 , CYS H:102 , GLU H:105 , HIS H:106
BINDING SITE FOR RESIDUE CO H 6002
18
BC9
SOFTWARE
HIS H:219 , HIS H:223 , HOH H:6108
BINDING SITE FOR RESIDUE CO H 6003
19
CC1
SOFTWARE
HIS I:79 , GLU I:83 , HIS I:98 , GLU I:172 , GLN I:175
BINDING SITE FOR RESIDUE CO I 7001
20
CC2
SOFTWARE
MET I:10 , CYS I:102 , GLU I:105 , HIS I:106
BINDING SITE FOR RESIDUE CO I 7002
21
CC3
SOFTWARE
HIS I:219 , HIS I:223 , HOH I:7111
BINDING SITE FOR RESIDUE CO I 7003
22
CC4
SOFTWARE
HIS J:79 , GLU J:83 , HIS J:98 , GLU J:172 , GLN J:175
BINDING SITE FOR RESIDUE CO J 8001
23
CC5
SOFTWARE
MET J:10 , CYS J:102 , GLU J:105 , HIS J:106
BINDING SITE FOR RESIDUE CO J 8002
24
CC6
SOFTWARE
HIS J:219 , HIS J:223 , HOH J:8109
BINDING SITE FOR RESIDUE CO J 8003
25
CC7
SOFTWARE
ASP A:35 , HOH A:1103 , DC F:19 , HOH F:37
BINDING SITE FOR RESIDUE NA A 1101
26
CC8
SOFTWARE
ASP B:35 , DC E:21
BINDING SITE FOR RESIDUE NA B 2102
27
CC9
SOFTWARE
ASP C:35 , DC E:16
BINDING SITE FOR RESIDUE NA C 3103
28
DC1
SOFTWARE
ASP D:35 , HOH D:4111 , DC F:24
BINDING SITE FOR RESIDUE NA D 4104
29
DC2
SOFTWARE
ASP G:35 , DC L:19 , HOH L:35 , HOH L:42
BINDING SITE FOR RESIDUE NA G 5105
30
DC3
SOFTWARE
ASP H:35 , HOH H:6109 , DC K:21
BINDING SITE FOR RESIDUE NA H 6106
31
DC4
SOFTWARE
ASP I:35 , DC K:16
BINDING SITE FOR RESIDUE NA I 7107
32
DC5
SOFTWARE
ASP J:35 , DC L:24 , HOH L:36
BINDING SITE FOR RESIDUE NA J 8108
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: HTH_DTXR (A:4-65,B:4-65,C:4-65,D:4-65,G:4-65...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HTH_DTXR
PS50944
DtxR-type HTH domain profile.
IDER_MYCTO
4-65
8
A:4-65
B:4-65
C:4-65
D:4-65
G:4-65
H:4-65
I:4-65
J:4-65
IDER_MYCTU
4-65
8
A:4-65
B:4-65
C:4-65
D:4-65
G:4-65
H:4-65
I:4-65
J:4-65
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 24)
Info
All SCOP Domains
1a: SCOP_d1u8ra1 (A:1-64)
1b: SCOP_d1u8rb1 (B:1-64)
1c: SCOP_d1u8rc1 (C:1-64)
1d: SCOP_d1u8rd1 (D:1-64)
1e: SCOP_d1u8rg1 (G:1-64)
1f: SCOP_d1u8rh1 (H:1-64)
1g: SCOP_d1u8ri1 (I:1-64)
1h: SCOP_d1u8rj1 (J:1-64)
2a: SCOP_d1u8ra2 (A:65-141)
2b: SCOP_d1u8rb2 (B:65-141)
2c: SCOP_d1u8rc2 (C:65-141)
2d: SCOP_d1u8rd2 (D:65-141)
2e: SCOP_d1u8rg2 (G:65-141)
2f: SCOP_d1u8rh2 (H:65-141)
2g: SCOP_d1u8ri2 (I:65-141)
2h: SCOP_d1u8rj2 (J:65-141)
3a: SCOP_d1u8ra3 (A:151-230)
3b: SCOP_d1u8ri3 (I:151-230)
3c: SCOP_d1u8rj3 (J:150-230)
3d: SCOP_d1u8rb3 (B:151-230)
3e: SCOP_d1u8rc3 (C:151-230)
3f: SCOP_d1u8rd3 (D:151-230)
3g: SCOP_d1u8rg3 (G:151-230)
3h: SCOP_d1u8rh3 (H:150-230)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Winged helix DNA-binding domain
(576)
Family
:
Iron-dependent repressor protein
(44)
Protein domain
:
Iron-dependent regulator IdeR
(6)
Mycobacterium tuberculosis [TaxId: 1773]
(6)
1a
d1u8ra1
A:1-64
1b
d1u8rb1
B:1-64
1c
d1u8rc1
C:1-64
1d
d1u8rd1
D:1-64
1e
d1u8rg1
G:1-64
1f
d1u8rh1
H:1-64
1g
d1u8ri1
I:1-64
1h
d1u8rj1
J:1-64
Fold
:
Iron-dependent repressor protein, dimerization domain
(45)
Superfamily
:
Iron-dependent repressor protein, dimerization domain
(45)
Family
:
Iron-dependent repressor protein, dimerization domain
(44)
Protein domain
:
Iron-dependent regulator
(6)
Mycobacterium tuberculosis [TaxId: 1773]
(6)
2a
d1u8ra2
A:65-141
2b
d1u8rb2
B:65-141
2c
d1u8rc2
C:65-141
2d
d1u8rd2
D:65-141
2e
d1u8rg2
G:65-141
2f
d1u8rh2
H:65-141
2g
d1u8ri2
I:65-141
2h
d1u8rj2
J:65-141
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
C-terminal domain of transcriptional repressors
(56)
Family
:
FeoA-like
(23)
Protein domain
:
Iron-dependent regulator IdeR
(2)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
3a
d1u8ra3
A:151-230
3b
d1u8ri3
I:151-230
3c
d1u8rj3
J:150-230
3d
d1u8rb3
B:151-230
3e
d1u8rc3
C:151-230
3f
d1u8rd3
D:151-230
3g
d1u8rg3
G:151-230
3h
d1u8rh3
H:150-230
[
close SCOP info
]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_1u8rA01 (A:1-73)
1b: CATH_1u8rB01 (B:1-73)
1c: CATH_1u8rC01 (C:1-73)
1d: CATH_1u8rD01 (D:1-73)
1e: CATH_1u8rG01 (G:1-73)
1f: CATH_1u8rH01 (H:1-73)
1g: CATH_1u8rI01 (I:1-73)
1h: CATH_1u8rJ01 (J:1-73)
2a: CATH_1u8rA02 (A:74-140)
2b: CATH_1u8rI02 (I:74-140)
2c: CATH_1u8rJ02 (J:74-140)
2d: CATH_1u8rB02 (B:74-140)
2e: CATH_1u8rC02 (C:74-140)
2f: CATH_1u8rD02 (D:74-140)
2g: CATH_1u8rG02 (G:74-140)
2h: CATH_1u8rH02 (H:74-140)
3a: CATH_1u8rA03 (A:151-230)
3b: CATH_1u8rB03 (B:151-230)
3c: CATH_1u8rC03 (C:151-230)
3d: CATH_1u8rD03 (D:151-230)
3e: CATH_1u8rG03 (G:151-230)
3f: CATH_1u8rH03 (H:151-230)
3g: CATH_1u8rI03 (I:151-230)
3h: CATH_1u8rJ03 (J:151-230)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
[unclassified]
(77)
1a
1u8rA01
A:1-73
1b
1u8rB01
B:1-73
1c
1u8rC01
C:1-73
1d
1u8rD01
D:1-73
1e
1u8rG01
G:1-73
1f
1u8rH01
H:1-73
1g
1u8rI01
I:1-73
1h
1u8rJ01
J:1-73
Topology
:
Diphtheria Toxin Repressor; domain 2
(34)
Homologous Superfamily
:
Diphtheria Toxin Repressor, domain 2
(32)
[unclassified]
(5)
2a
1u8rA02
A:74-140
2b
1u8rI02
I:74-140
2c
1u8rJ02
J:74-140
2d
1u8rB02
B:74-140
2e
1u8rC02
C:74-140
2f
1u8rD02
D:74-140
2g
1u8rG02
G:74-140
2h
1u8rH02
H:74-140
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
SH3 type barrels.
(648)
Homologous Superfamily
:
[code=2.30.30.90, no name defined]
(14)
[unclassified]
(1)
3a
1u8rA03
A:151-230
3b
1u8rB03
B:151-230
3c
1u8rC03
C:151-230
3d
1u8rD03
D:151-230
3e
1u8rG03
G:151-230
3f
1u8rH03
H:151-230
3g
1u8rI03
I:151-230
3h
1u8rJ03
J:151-230
[
close CATH info
]
Pfam Domains
(3, 24)
Info
all PFAM domains
1a: PFAM_Fe_dep_repr_C_1u8rJ01 (J:65-135)
1b: PFAM_Fe_dep_repr_C_1u8rJ02 (J:65-135)
1c: PFAM_Fe_dep_repr_C_1u8rJ03 (J:65-135)
1d: PFAM_Fe_dep_repr_C_1u8rJ04 (J:65-135)
1e: PFAM_Fe_dep_repr_C_1u8rJ05 (J:65-135)
1f: PFAM_Fe_dep_repr_C_1u8rJ06 (J:65-135)
1g: PFAM_Fe_dep_repr_C_1u8rJ07 (J:65-135)
1h: PFAM_Fe_dep_repr_C_1u8rJ08 (J:65-135)
2a: PFAM_Fe_dep_repress_1u8rJ09 (J:3-62)
2b: PFAM_Fe_dep_repress_1u8rJ10 (J:3-62)
2c: PFAM_Fe_dep_repress_1u8rJ11 (J:3-62)
2d: PFAM_Fe_dep_repress_1u8rJ12 (J:3-62)
2e: PFAM_Fe_dep_repress_1u8rJ13 (J:3-62)
2f: PFAM_Fe_dep_repress_1u8rJ14 (J:3-62)
2g: PFAM_Fe_dep_repress_1u8rJ15 (J:3-62)
2h: PFAM_Fe_dep_repress_1u8rJ16 (J:3-62)
3a: PFAM_FeoA_1u8rJ17 (J:152-229)
3b: PFAM_FeoA_1u8rJ18 (J:152-229)
3c: PFAM_FeoA_1u8rJ19 (J:152-229)
3d: PFAM_FeoA_1u8rJ20 (J:152-229)
3e: PFAM_FeoA_1u8rJ21 (J:152-229)
3f: PFAM_FeoA_1u8rJ22 (J:152-229)
3g: PFAM_FeoA_1u8rJ23 (J:152-229)
3h: PFAM_FeoA_1u8rJ24 (J:152-229)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HTH
(544)
Family
:
Fe_dep_repr_C
(11)
Mycobacterium tuberculosis
(1)
1a
Fe_dep_repr_C-1u8rJ01
J:65-135
1b
Fe_dep_repr_C-1u8rJ02
J:65-135
1c
Fe_dep_repr_C-1u8rJ03
J:65-135
1d
Fe_dep_repr_C-1u8rJ04
J:65-135
1e
Fe_dep_repr_C-1u8rJ05
J:65-135
1f
Fe_dep_repr_C-1u8rJ06
J:65-135
1g
Fe_dep_repr_C-1u8rJ07
J:65-135
1h
Fe_dep_repr_C-1u8rJ08
J:65-135
Family
:
Fe_dep_repress
(10)
Mycobacterium tuberculosis
(1)
2a
Fe_dep_repress-1u8rJ09
J:3-62
2b
Fe_dep_repress-1u8rJ10
J:3-62
2c
Fe_dep_repress-1u8rJ11
J:3-62
2d
Fe_dep_repress-1u8rJ12
J:3-62
2e
Fe_dep_repress-1u8rJ13
J:3-62
2f
Fe_dep_repress-1u8rJ14
J:3-62
2g
Fe_dep_repress-1u8rJ15
J:3-62
2h
Fe_dep_repress-1u8rJ16
J:3-62
Clan
:
TRB
(15)
Family
:
FeoA
(11)
Mycobacterium tuberculosis
(1)
3a
FeoA-1u8rJ17
J:152-229
3b
FeoA-1u8rJ18
J:152-229
3c
FeoA-1u8rJ19
J:152-229
3d
FeoA-1u8rJ20
J:152-229
3e
FeoA-1u8rJ21
J:152-229
3f
FeoA-1u8rJ22
J:152-229
3g
FeoA-1u8rJ23
J:152-229
3h
FeoA-1u8rJ24
J:152-229
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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