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3IAS
Biol. Unit 1
Info
Asym.Unit (1.5 MB)
Biol.Unit 1 (396 KB)
Biol.Unit 2 (395 KB)
Biol.Unit 3 (397 KB)
Biol.Unit 4 (396 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE HYDROPHILIC DOMAIN OF RESPIRATORY COMPLEX I FROM THERMUS THERMOPHILUS, OXIDIZED, 4 MOL/ASU, RE-REFINED TO 3.15 ANGSTROM RESOLUTION
Authors
:
L. A. Sazanov, J. M. Berrisford
Date
:
14 Jul 09 (Deposition) - 15 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.15
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,J,K,L,M,N,O,P,Q,S,T,U,V,W,X,Y,Z,1,2,3,4,5,6,7,9
Biol. Unit 1: 1,2,3,4,5,6,7,9 (1x)
Biol. Unit 2: A,B,C,D,E,F,G,H (1x)
Biol. Unit 3: J,K,L,M,N,O,P,Q (1x)
Biol. Unit 4: S,T,U,V,W,X,Y,Z (1x)
Keywords
:
Oxidoreductase, Electron Transport, Respiratory Chain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Berrisford, L. A. Sazanov
Structural Basis For The Mechanism Of Respiratory Complex I
J. Biol. Chem. V. 284 29773 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
2a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2b: FE2/S2 (INORGANIC) CLUSTER (FESb)
2c: FE2/S2 (INORGANIC) CLUSTER (FESc)
2d: FE2/S2 (INORGANIC) CLUSTER (FESd)
2e: FE2/S2 (INORGANIC) CLUSTER (FESe)
2f: FE2/S2 (INORGANIC) CLUSTER (FESf)
2g: FE2/S2 (INORGANIC) CLUSTER (FESg)
2h: FE2/S2 (INORGANIC) CLUSTER (FESh)
3a: FLAVIN MONONUCLEOTIDE (FMNa)
3b: FLAVIN MONONUCLEOTIDE (FMNb)
3c: FLAVIN MONONUCLEOTIDE (FMNc)
3d: FLAVIN MONONUCLEOTIDE (FMNd)
4a: IRON/SULFUR CLUSTER (SF4a)
4aa: IRON/SULFUR CLUSTER (SF4aa)
4ab: IRON/SULFUR CLUSTER (SF4ab)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
4e: IRON/SULFUR CLUSTER (SF4e)
4f: IRON/SULFUR CLUSTER (SF4f)
4g: IRON/SULFUR CLUSTER (SF4g)
4h: IRON/SULFUR CLUSTER (SF4h)
4i: IRON/SULFUR CLUSTER (SF4i)
4j: IRON/SULFUR CLUSTER (SF4j)
4k: IRON/SULFUR CLUSTER (SF4k)
4l: IRON/SULFUR CLUSTER (SF4l)
4m: IRON/SULFUR CLUSTER (SF4m)
4n: IRON/SULFUR CLUSTER (SF4n)
4o: IRON/SULFUR CLUSTER (SF4o)
4p: IRON/SULFUR CLUSTER (SF4p)
4q: IRON/SULFUR CLUSTER (SF4q)
4r: IRON/SULFUR CLUSTER (SF4r)
4s: IRON/SULFUR CLUSTER (SF4s)
4t: IRON/SULFUR CLUSTER (SF4t)
4u: IRON/SULFUR CLUSTER (SF4u)
4v: IRON/SULFUR CLUSTER (SF4v)
4w: IRON/SULFUR CLUSTER (SF4w)
4x: IRON/SULFUR CLUSTER (SF4x)
4y: IRON/SULFUR CLUSTER (SF4y)
4z: IRON/SULFUR CLUSTER (SF4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
3
FMN
1
Ligand/Ion
FLAVIN MONONUCLEOTIDE
4
SF4
7
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG 4:84 , HIS 4:169 , CYS 6:45 , CYS 6:46 , GLY 6:82 , ARG 6:83 , ALA 6:110 , CYS 6:111 , CYS 6:140 , PRO 6:141
BINDING SITE FOR RESIDUE SF4 6 182
02
AC2
SOFTWARE
HIS 9:41 , CYS 9:63 , PRO 9:64 , ILE 9:68 , CYS 9:98 , ILE 9:99 , PHE 9:100 , CYS 9:101 , GLY 9:102 , CYS 9:104
BINDING SITE FOR RESIDUE SF4 9 183
03
AC3
SOFTWARE
CYS 9:53 , ILE 9:54 , CYS 9:56 , SER 9:57 , CYS 9:59 , CYS 9:108 , PRO 9:109 , THR 9:110
BINDING SITE FOR RESIDUE SF4 9 184
04
AC4
SOFTWARE
HIS 3:115 , ASP 3:118 , CYS 3:119 , CYS 3:122 , LYS 3:124 , CYS 3:128 , GLN 3:131 , VAL 3:232 , GLY 3:233
BINDING SITE FOR RESIDUE SF4 3 784
05
AC5
SOFTWARE
CYS 3:181 , ILE 3:182 , CYS 3:184 , CYS 3:187 , CYS 3:230 , LEU 3:235
BINDING SITE FOR RESIDUE SF4 3 785
06
AC6
SOFTWARE
CYS 3:256 , LEU 3:258 , CYS 3:259 , VAL 3:261 , GLY 3:262 , CYS 3:263 , ILE 3:290 , CYS 3:291 , PRO 3:407 , ILE 3:408
BINDING SITE FOR RESIDUE SF4 3 786
07
AC7
SOFTWARE
CYS 3:34 , SER 3:35 , CYS 3:45 , ARG 3:46 , CYS 3:48 , CYS 3:83
BINDING SITE FOR RESIDUE FES 3 787
08
AC8
SOFTWARE
PRO 1:199 , SER 1:352 , CYS 1:353 , GLY 1:354 , LYS 1:355 , CYS 1:356 , CYS 1:359 , CYS 1:400
BINDING SITE FOR RESIDUE SF4 1 439
09
AC9
SOFTWARE
CYS 2:83 , SER 2:87 , CYS 2:88 , CYS 2:124 , LEU 2:125 , GLY 2:126 , SER 2:127 , CYS 2:128
BINDING SITE FOR RESIDUE FES 2 182
10
BC1
SOFTWARE
GLY 1:64 , GLY 1:66 , ALA 1:68 , THR 1:72 , LYS 1:75 , ASN 1:92 , ASP 1:94 , SER 1:96 , TYR 1:180 , GLY 1:183 , GLU 1:184 , GLU 1:185 , ILE 1:218 , ASN 1:219 , ASN 1:220 , THR 1:223 , PRO 1:401
BINDING SITE FOR RESIDUE FMN 1 440
11
BC2
SOFTWARE
LEU 3:274 , ASP 3:302
BINDING SITE FOR RESIDUE CA 3 788
12
BC3
SOFTWARE
ASP 2:9
BINDING SITE FOR RESIDUE CA 2 202
13
BC4
SOFTWARE
ASP 3:165 , HIS 3:168 , GLU 7:32 , GLY 7:64
BINDING SITE FOR RESIDUE CA 3 789
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(13, 15)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
NQO3_THET8
1-99
1
3:1-99
-
-
-
2
COMPLEX1_75K_1
PS00641
Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1.
NQO3_THET8
31-48
1
3:31-48
-
-
-
3
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
NQO9_THET8
43-73
89-118
2
9:43-73
-
-
-
9:89-118
-
-
-
4
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
NQO9_THET8
53-64
98-109
2
9:53-64
-
-
-
9:98-109
-
-
-
5
COMPLEX1_49K
PS00535
Respiratory chain NADH dehydrogenase 49 Kd subunit signature.
NQO4_THET8
62-73
1
4:62-73
-
-
-
6
COMPLEX1_24K
PS01099
Respiratory-chain NADH dehydrogenase 24 Kd subunit signature.
NQO2_THET8
114-132
1
2:114-132
-
-
-
7
COMPLEX1_30K
PS00542
Respiratory chain NADH dehydrogenase 30 Kd subunit signature.
NQO5_THET8
115-136
1
5:115-136
-
-
-
8
COMPLEX1_75K_2
PS00642
Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2.
NQO3_THET8
119-131
1
3:119-131
-
-
-
9
COMPLEX1_20K
PS01150
Respiratory-chain NADH dehydrogenase 20 Kd subunit signature.
NQO6_THET8
126-142
1
6:126-142
-
-
-
10
COMPLEX1_51K_1
PS00644
Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1.
NQO1_THET8
176-191
1
1:176-191
-
-
-
11
COMPLEX1_75K_3
PS00643
Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3.
NQO3_THET8
180-190
1
3:180-190
-
-
-
12
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
NQO3_THET8
249-305
1
3:249-305
-
-
-
13
COMPLEX1_51K_2
PS00645
Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2.
NQO1_THET8
351-362
1
1:351-362
-
-
-
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(13, 52)
Info
All SCOP Domains
01a: SCOP_d3ias13 (1:334-438)
01b: SCOP_d3iasa3 (A:334-438)
01c: SCOP_d3iasj3 (J:334-438)
01d: SCOP_d3iass3 (S:334-438)
02a: SCOP_d3ias34 (3:686-777)
02b: SCOP_d3iasc4 (C:686-777)
02c: SCOP_d3iasl4 (L:686-777)
02d: SCOP_d3iasu4 (U:686-777)
03a: SCOP_d3ias31 (3:1-95)
03b: SCOP_d3iasc1 (C:1-95)
03c: SCOP_d3iasl1 (L:1-95)
03d: SCOP_d3iasu1 (U:1-95)
04a: SCOP_d3ias12 (1:250-333)
04b: SCOP_d3iasa2 (A:250-333)
04c: SCOP_d3iasj2 (J:250-333)
04d: SCOP_d3iass2 (S:250-333)
05a: SCOP_d3ias32 (3:96-246)
05b: SCOP_d3iasc2 (C:96-246)
05c: SCOP_d3iasl2 (L:96-246)
05d: SCOP_d3iasu2 (U:96-246)
06a: SCOP_d3ias9_ (9:)
06b: SCOP_d3iasg_ (G:)
06c: SCOP_d3iasp_ (P:)
06d: SCOP_d3iasy_ (Y:)
07a: SCOP_d3ias7_ (7:)
07b: SCOP_d3iash_ (H:)
07c: SCOP_d3iasq_ (Q:)
07d: SCOP_d3iasz_ (Z:)
08a: SCOP_d3ias5_ (5:)
08b: SCOP_d3iase_ (E:)
08c: SCOP_d3iasn_ (N:)
08d: SCOP_d3iasw_ (W:)
09a: SCOP_d3ias33 (3:247-685)
09b: SCOP_d3iasc3 (C:247-685)
09c: SCOP_d3iasl3 (L:247-685)
09d: SCOP_d3iasu3 (U:247-685)
10a: SCOP_d3ias11 (1:2-249)
10b: SCOP_d3iasa1 (A:2-249)
10c: SCOP_d3iasj1 (J:2-249)
10d: SCOP_d3iass1 (S:2-249)
11a: SCOP_d3ias2_ (2:)
11b: SCOP_d3iasb_ (B:)
11c: SCOP_d3iask_ (K:)
11d: SCOP_d3iast_ (T:)
12a: SCOP_d3ias6_ (6:)
12b: SCOP_d3iasf_ (F:)
12c: SCOP_d3iaso_ (O:)
12d: SCOP_d3iasx_ (X:)
13a: SCOP_d3ias4_ (4:)
13b: SCOP_d3iasd_ (D:)
13c: SCOP_d3iasm_ (M:)
13d: SCOP_d3iasv_ (V:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Nqo1C-terminal domain-like
(4)
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
01a
d3ias13
1:334-438
01b
d3iasa3
A:334-438
01c
d3iasj3
J:334-438
01d
d3iass3
S:334-438
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
automated matches
(19)
Protein domain
:
automated matches
(19)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
02a
d3ias34
3:686-777
02b
d3iasc4
C:686-777
02c
d3iasl4
L:686-777
02d
d3iasu4
U:686-777
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
automated matches
(18)
Protein domain
:
automated matches
(18)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
03a
d3ias31
3:1-95
03b
d3iasc1
C:1-95
03c
d3iasl1
L:1-95
03d
d3iasu1
U:1-95
Superfamily
:
Nqo1 middle domain-like
(4)
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
04a
d3ias12
1:250-333
04b
d3iasa2
A:250-333
04c
d3iasj2
J:250-333
04d
d3iass2
S:250-333
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
automated matches
(4)
Protein domain
:
automated matches
(4)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
05a
d3ias32
3:96-246
05b
d3iasc2
C:96-246
05c
d3iasl2
L:96-246
05d
d3iasu2
U:96-246
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
automated matches
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
06a
d3ias9_
9:
06b
d3iasg_
G:
06c
d3iasp_
P:
06d
d3iasy_
Y:
Fold
:
N domain of copper amine oxidase-like
(44)
Superfamily
:
Frataxin/Nqo15-like
(24)
Family
:
Nqo15-like
(4)
Protein domain
:
NADH-quinone oxidoreductase subunit 15, Nqo15
(4)
Thermus thermophilus [TaxId: 274]
(4)
07a
d3ias7_
7:
07b
d3iash_
H:
07c
d3iasq_
Q:
07d
d3iasz_
Z:
Fold
:
Nqo5-like
(4)
Superfamily
:
Nqo5-like
(4)
Family
:
Nqo5-like
(4)
Protein domain
:
automated matches
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
08a
d3ias5_
5:
08b
d3iase_
E:
08c
d3iasn_
N:
08d
d3iasw_
W:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
automated matches
(12)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
09a
d3ias33
3:247-685
09b
d3iasc3
C:247-685
09c
d3iasl3
L:247-685
09d
d3iasu3
U:247-685
Fold
:
Nqo1 FMN-binding domain-like
(4)
Superfamily
:
Nqo1 FMN-binding domain-like
(4)
Family
:
Nqo1 FMN-binding domain-like
(4)
Protein domain
:
automated matches
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
10a
d3ias11
1:2-249
10b
d3iasa1
A:2-249
10c
d3iasj1
J:2-249
10d
d3iass1
S:2-249
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
NQO2-like
(4)
Protein domain
:
automated matches
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
11a
d3ias2_
2:
11b
d3iasb_
B:
11c
d3iask_
K:
11d
d3iast_
T:
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
HydA/Nqo6-like
(51)
Superfamily
:
HydA/Nqo6-like
(51)
Family
:
Nq06-like
(4)
Protein domain
:
automated matches
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
12a
d3ias6_
6:
12b
d3iasf_
F:
12c
d3iaso_
O:
12d
d3iasx_
X:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nqo4-like
(4)
Protein domain
:
automated matches
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(3)
13a
d3ias4_
4:
13b
d3iasd_
D:
13c
d3iasm_
M:
13d
d3iasv_
V:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
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Chain 9
Asymmetric Unit 1
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Miscellaneous
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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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