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1BCF
Biol. Unit 1
Info
Asym.Unit (321 KB)
Biol.Unit 1 (618 KB)
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(1)
Title
:
THE STRUCTURE OF A UNIQUE, TWO-FOLD SYMMETRIC, HAEM-BINDING SITE
Authors
:
F. Frolow, A. J. Kalb(Gilboa), J. Yariv
Date
:
06 Dec 93 (Deposition) - 20 Dec 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (2x)
Keywords
:
Iron Storage And Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Frolow, A. J. Kalb, J. Yariv
Structure Of A Unique Twofold Symmetric Haem-Binding Site.
Nat. Struct. Biol. V. 1 453 1994
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 12)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
1e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
1f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
2i: MANGANESE (II) ION (MNi)
2j: MANGANESE (II) ION (MNj)
2k: MANGANESE (II) ION (MNk)
2l: MANGANESE (II) ION (MNl)
2m: MANGANESE (II) ION (MNm)
2n: MANGANESE (II) ION (MNn)
2o: MANGANESE (II) ION (MNo)
2p: MANGANESE (II) ION (MNp)
2q: MANGANESE (II) ION (MNq)
2r: MANGANESE (II) ION (MNr)
2s: MANGANESE (II) ION (MNs)
2t: MANGANESE (II) ION (MNt)
2u: MANGANESE (II) ION (MNu)
2v: MANGANESE (II) ION (MNv)
2w: MANGANESE (II) ION (MNw)
2x: MANGANESE (II) ION (MNx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
12
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(54, 54)
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: MA1 (UNKNOWN)
32: MA2 (UNKNOWN)
33: MB1 (UNKNOWN)
34: MB2 (UNKNOWN)
35: MC1 (UNKNOWN)
36: MC2 (UNKNOWN)
37: MD1 (UNKNOWN)
38: MD2 (UNKNOWN)
39: ME1 (UNKNOWN)
40: ME2 (UNKNOWN)
41: MF1 (UNKNOWN)
42: MF2 (UNKNOWN)
43: MG1 (UNKNOWN)
44: MG2 (UNKNOWN)
45: MH1 (UNKNOWN)
46: MH2 (UNKNOWN)
47: MI1 (UNKNOWN)
48: MI2 (UNKNOWN)
49: MJ1 (UNKNOWN)
50: MJ2 (UNKNOWN)
51: MK1 (UNKNOWN)
52: MK2 (UNKNOWN)
53: ML1 (UNKNOWN)
54: ML2 (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:51 , GLU A:94 , GLU A:127 , HIS A:130
BINDING SITE FOR RESIDUE MN A 600
02
AC2
SOFTWARE
GLU A:18 , GLU A:51 , HIS A:54 , GLU A:127
BINDING SITE FOR RESIDUE MN A 601
03
AC3
SOFTWARE
GLU B:51 , GLU B:94 , GLU B:127 , HIS B:130
BINDING SITE FOR RESIDUE MN B 600
04
AC4
SOFTWARE
GLU B:18 , GLU B:51 , HIS B:54 , GLU B:127
BINDING SITE FOR RESIDUE MN B 601
05
AC5
SOFTWARE
GLU C:51 , GLU C:94 , GLU C:127 , HIS C:130
BINDING SITE FOR RESIDUE MN C 600
06
AC6
SOFTWARE
GLU C:18 , GLU C:51 , HIS C:54 , GLU C:127
BINDING SITE FOR RESIDUE MN C 601
07
AC7
SOFTWARE
GLU D:51 , GLU D:94 , GLU D:127 , HIS D:130
BINDING SITE FOR RESIDUE MN D 600
08
AC8
SOFTWARE
GLU D:18 , GLU D:51 , HIS D:54 , GLU D:127
BINDING SITE FOR RESIDUE MN D 601
09
AC9
SOFTWARE
GLU E:51 , GLU E:94 , GLU E:127 , HIS E:130
BINDING SITE FOR RESIDUE MN E 600
10
BC1
SOFTWARE
GLU E:18 , GLU E:51 , HIS E:54 , GLU E:127
BINDING SITE FOR RESIDUE MN E 601
11
BC2
SOFTWARE
GLU F:51 , GLU F:94 , GLU F:127 , HIS F:130
BINDING SITE FOR RESIDUE MN F 600
12
BC3
SOFTWARE
GLU F:18 , GLU F:51 , HIS F:54 , GLU F:127
BINDING SITE FOR RESIDUE MN F 601
13
BC4
SOFTWARE
GLU G:51 , GLU G:94 , GLU G:127 , HIS G:130
BINDING SITE FOR RESIDUE MN G 600
14
BC5
SOFTWARE
GLU G:18 , GLU G:51 , HIS G:54 , GLU G:127
BINDING SITE FOR RESIDUE MN G 601
15
BC6
SOFTWARE
GLU H:51 , GLU H:94 , GLU H:127 , HIS H:130
BINDING SITE FOR RESIDUE MN H 600
16
BC7
SOFTWARE
GLU H:18 , GLU H:51 , HIS H:54 , GLU H:127
BINDING SITE FOR RESIDUE MN H 601
17
BC8
SOFTWARE
GLU I:51 , GLU I:94 , GLU I:127 , HIS I:130
BINDING SITE FOR RESIDUE MN I 600
18
BC9
SOFTWARE
GLU I:18 , GLU I:51 , HIS I:54 , GLU I:127
BINDING SITE FOR RESIDUE MN I 601
19
CC1
SOFTWARE
GLU J:51 , GLU J:94 , GLU J:127 , HIS J:130
BINDING SITE FOR RESIDUE MN J 600
20
CC2
SOFTWARE
GLU J:18 , GLU J:51 , HIS J:54 , GLU J:127
BINDING SITE FOR RESIDUE MN J 601
21
CC3
SOFTWARE
GLU K:51 , GLU K:94 , GLU K:127 , HIS K:130
BINDING SITE FOR RESIDUE MN K 600
22
CC4
SOFTWARE
GLU K:18 , GLU K:51 , HIS K:54 , GLU K:127
BINDING SITE FOR RESIDUE MN K 601
23
CC5
SOFTWARE
GLU L:51 , GLU L:94 , GLU L:127 , HIS L:130
BINDING SITE FOR RESIDUE MN L 600
24
CC6
SOFTWARE
GLU L:18 , GLU L:51 , HIS L:54 , GLU L:127
BINDING SITE FOR RESIDUE MN L 601
25
CC7
SOFTWARE
ASN A:23 , TYR A:45 , MET A:52 , ILE A:59 , LEU B:19 , ASN B:23 , PHE B:26 , MET B:52 , LYS B:53
BINDING SITE FOR RESIDUE HEM A 200
26
CC8
SOFTWARE
ASN C:23 , TYR C:45 , MET C:52 , ILE C:59 , LEU D:19 , ASN D:23 , PHE D:26 , MET D:52 , LYS D:53
BINDING SITE FOR RESIDUE HEM C 201
27
CC9
SOFTWARE
ASN E:23 , TYR E:45 , MET E:52 , ILE E:59 , LEU F:19 , ASN F:23 , PHE F:26 , MET F:52 , LYS F:53
BINDING SITE FOR RESIDUE HEM E 202
28
DC1
SOFTWARE
ASN G:23 , TYR G:45 , MET G:52 , ILE G:59 , LEU H:19 , ASN H:23 , PHE H:26 , MET H:52 , LYS H:53
BINDING SITE FOR RESIDUE HEM G 203
29
DC2
SOFTWARE
ASN I:23 , TYR I:45 , MET I:52 , ILE I:59 , LEU J:19 , ASN J:23 , PHE J:26 , MET J:52 , LYS J:53
BINDING SITE FOR RESIDUE HEM I 204
30
DC3
SOFTWARE
ASN K:23 , TYR K:45 , MET K:52 , ILE K:59 , LEU L:19 , ASN L:23 , PHE L:26 , MET L:52 , LYS L:53
BINDING SITE FOR RESIDUE HEM K 205
31
MA1
UNKNOWN
GLU A:18 , GLU A:51 , HIS A:54 , GLU A:127
NULL
32
MA2
UNKNOWN
GLU A:51 , GLU A:94 , GLU A:127 , HIS A:130
NULL
33
MB1
UNKNOWN
GLU B:18 , GLU B:51 , HIS B:54 , GLU B:127
NULL
34
MB2
UNKNOWN
GLU B:51 , GLU B:94 , GLU B:127 , HIS B:130
NULL
35
MC1
UNKNOWN
GLU C:18 , GLU C:51 , HIS C:54 , GLU C:127
NULL
36
MC2
UNKNOWN
GLU C:51 , GLU C:94 , GLU C:127 , HIS C:130
NULL
37
MD1
UNKNOWN
GLU D:18 , GLU D:51 , HIS D:54 , GLU D:127
NULL
38
MD2
UNKNOWN
GLU D:51 , GLU D:94 , GLU D:127 , HIS D:130
NULL
39
ME1
UNKNOWN
GLU E:18 , GLU E:51 , HIS E:54 , GLU E:127
NULL
40
ME2
UNKNOWN
GLU E:51 , GLU E:94 , GLU E:127 , HIS E:130
NULL
41
MF1
UNKNOWN
GLU F:18 , GLU F:51 , HIS F:54 , GLU F:127
NULL
42
MF2
UNKNOWN
GLU F:51 , GLU F:94 , GLU F:127 , HIS F:130
NULL
43
MG1
UNKNOWN
GLU G:18 , GLU G:51 , HIS G:54 , GLU G:127
NULL
44
MG2
UNKNOWN
GLU G:51 , GLU G:94 , GLU G:127 , HIS G:130
NULL
45
MH1
UNKNOWN
GLU H:18 , GLU H:51 , HIS H:54 , GLU H:127
NULL
46
MH2
UNKNOWN
GLU H:51 , GLU H:94 , GLU H:127 , HIS H:130
NULL
47
MI1
UNKNOWN
GLU I:18 , GLU I:51 , HIS I:54 , GLU I:127
NULL
48
MI2
UNKNOWN
GLU I:51 , GLU I:94 , GLU I:127 , HIS I:130
NULL
49
MJ1
UNKNOWN
GLU J:18 , GLU J:51 , HIS J:54 , GLU J:127
NULL
50
MJ2
UNKNOWN
GLU J:51 , GLU J:94 , GLU J:127 , HIS J:130
NULL
51
MK1
UNKNOWN
GLU K:18 , GLU K:51 , HIS K:54 , GLU K:127
NULL
52
MK2
UNKNOWN
GLU K:51 , GLU K:94 , GLU K:127 , HIS K:130
NULL
53
ML1
UNKNOWN
GLU L:18 , GLU L:51 , HIS L:54 , GLU L:127
NULL
54
ML2
UNKNOWN
GLU L:51 , GLU L:94 , GLU L:127 , HIS L:130
NULL
[
close Site info
]
SAPs(SNPs)/Variants
(10, 240)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_BFR_ECOLI_001 (K38M, chain A/B/C/D/E/F/G/H/I/J/K/L, )
02: VAR_BFR_ECOLI_002 (R57K, chain A/B/C/D/E/F/G/H/I/J/K/L, )
03: VAR_BFR_ECOLI_003 (L68I, chain A/B/C/D/E/F/G/H/I/J/K/L, )
04: VAR_BFR_ECOLI_004 (N78G, chain A/B/C/D/E/F/G/H/I/J/K/L, )
05: VAR_BFR_ECOLI_005 (R88Q, chain A/B/C/D/E/F/G/H/I/J/K/L, )
06: VAR_BFR_ECOLI_006 (A92R, chain A/B/C/D/E/F/G/H/I/J/K/L, )
07: VAR_BFR_ECOLI_007 (D96E, chain A/B/C/D/E/F/G/H/I/J/K/L, )
08: VAR_BFR_ECOLI_008 (N100D, chain A/B/C/D/E/F/G/H/I/J/K/L, )
09: VAR_BFR_ECOLI_009 (G106A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
10: VAR_BFR_ECOLI_010 (R125A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_BFR_ECOLI_001
*
K
38
M
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
K
38
M
02
UniProt
VAR_BFR_ECOLI_002
*
R
57
K
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
57
K
03
UniProt
VAR_BFR_ECOLI_003
*
L
68
I
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
L
68
I
04
UniProt
VAR_BFR_ECOLI_004
*
N
78
G
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
N
78
G
05
UniProt
VAR_BFR_ECOLI_005
*
R
88
Q
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
88
Q
06
UniProt
VAR_BFR_ECOLI_006
*
A
92
R
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
A
92
R
07
UniProt
VAR_BFR_ECOLI_007
*
D
96
E
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
D
96
E
08
UniProt
VAR_BFR_ECOLI_008
*
N
100
D
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
N
100
D
09
UniProt
VAR_BFR_ECOLI_009
*
G
106
A
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
G
106
A
10
UniProt
VAR_BFR_ECOLI_010
*
R
125
A
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
125
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 48)
Info
All PROSITE Patterns/Profiles
1: BACTERIOFERRITIN (A:1-19,B:1-19,C:1-19,D:1-19,E:1-19...)
2: FERRITIN_LIKE (A:1-145,B:1-145,C:1-145,D:1-145,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIOFERRITIN
PS00549
Bacterioferritin signature.
BFR_ECOLI
1-19
24
A:1-19
B:1-19
C:1-19
D:1-19
E:1-19
F:1-19
G:1-19
H:1-19
I:1-19
J:1-19
K:1-19
L:1-19
2
FERRITIN_LIKE
PS50905
Ferritin-like diiron domain profile.
BFR_ECOLI
1-145
24
A:1-145
B:1-145
C:1-145
D:1-145
E:1-145
F:1-145
G:1-145
H:1-145
I:1-145
J:1-145
K:1-145
L:1-145
[
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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1bcfa_ (A:)
1b: SCOP_d1bcfb_ (B:)
1c: SCOP_d1bcfc_ (C:)
1d: SCOP_d1bcfd_ (D:)
1e: SCOP_d1bcfe_ (E:)
1f: SCOP_d1bcff_ (F:)
1g: SCOP_d1bcfg_ (G:)
1h: SCOP_d1bcfh_ (H:)
1i: SCOP_d1bcfi_ (I:)
1j: SCOP_d1bcfj_ (J:)
1k: SCOP_d1bcfk_ (K:)
1l: SCOP_d1bcfl_ (L:)
View:
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
Bacterioferritin (cytochrome b1)
(19)
Escherichia coli [TaxId: 562]
(11)
1a
d1bcfa_
A:
1b
d1bcfb_
B:
1c
d1bcfc_
C:
1d
d1bcfd_
D:
1e
d1bcfe_
E:
1f
d1bcff_
F:
1g
d1bcfg_
G:
1h
d1bcfh_
H:
1i
d1bcfi_
I:
1j
d1bcfj_
J:
1k
d1bcfk_
K:
1l
d1bcfl_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1bcfA00 (A:1-158)
1b: CATH_1bcfB00 (B:1-158)
1c: CATH_1bcfK00 (K:1-158)
1d: CATH_1bcfL00 (L:1-158)
1e: CATH_1bcfC00 (C:1-158)
1f: CATH_1bcfD00 (D:1-158)
1g: CATH_1bcfE00 (E:1-158)
1h: CATH_1bcfF00 (F:1-158)
1i: CATH_1bcfG00 (G:1-158)
1j: CATH_1bcfH00 (H:1-158)
1k: CATH_1bcfI00 (I:1-158)
1l: CATH_1bcfJ00 (J:1-158)
View:
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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Escherichia coli. Organism_taxid: 562
(2)
1a
1bcfA00
A:1-158
1b
1bcfB00
B:1-158
1c
1bcfK00
K:1-158
1d
1bcfL00
L:1-158
1e
1bcfC00
C:1-158
1f
1bcfD00
D:1-158
1g
1bcfE00
E:1-158
1h
1bcfF00
F:1-158
1i
1bcfG00
G:1-158
1j
1bcfH00
H:1-158
1k
1bcfI00
I:1-158
1l
1bcfJ00
J:1-158
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
Asymmetric Unit 2
Rendering
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by Chain (Biol. Unit)
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(e.g.: "#3cb371" or "60,179,113")
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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)
[
close Script example commands
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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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