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1SQ3
Biol. Unit 1
Info
Asym.Unit (357 KB)
Biol.Unit 1 (665 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF A NOVEL OPEN PORE FERRITIN FROM THE HYPERTHERMOPHILIC ARCHAEON ARCHAEOGLOBUS FULGIDUS.
Authors
:
E. Johnson, D. Cascio, S. Michael, I. Schroder
Date
:
17 Mar 04 (Deposition) - 12 Apr 05 (Release) - 05 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
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
:
Ferroxidase, Four Helix Bundle, Iron Storage, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Johnson, D. Cascio, M. R. Sawaya, M. Gingery, I. Schroder
Crystal Structures Of A Tetrahedral Open Pore Ferritin From The Hyperthermophilic Archaeon Archaeoglobus Fulgidus.
Structure V. 13 637 2005
[
close entry info
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Hetero Components
(1, 192)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1aa: FE (III) ION (FEaa)
1ab: FE (III) ION (FEab)
1ac: FE (III) ION (FEac)
1ad: FE (III) ION (FEad)
1ae: FE (III) ION (FEae)
1af: FE (III) ION (FEaf)
1ag: FE (III) ION (FEag)
1ah: FE (III) ION (FEah)
1ai: FE (III) ION (FEai)
1aj: FE (III) ION (FEaj)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
1e: FE (III) ION (FEe)
1f: FE (III) ION (FEf)
1g: FE (III) ION (FEg)
1h: FE (III) ION (FEh)
1i: FE (III) ION (FEi)
1j: FE (III) ION (FEj)
1k: FE (III) ION (FEk)
1l: FE (III) ION (FEl)
1m: FE (III) ION (FEm)
1n: FE (III) ION (FEn)
1o: FE (III) ION (FEo)
1p: FE (III) ION (FEp)
1q: FE (III) ION (FEq)
1r: FE (III) ION (FEr)
1s: FE (III) ION (FEs)
1t: FE (III) ION (FEt)
1u: FE (III) ION (FEu)
1v: FE (III) ION (FEv)
1w: FE (III) ION (FEw)
1x: FE (III) ION (FEx)
1y: FE (III) ION (FEy)
1z: FE (III) ION (FEz)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2ao: SELENOMETHIONINE (MSEao)
2ap: SELENOMETHIONINE (MSEap)
2aq: SELENOMETHIONINE (MSEaq)
2ar: SELENOMETHIONINE (MSEar)
2as: SELENOMETHIONINE (MSEas)
2at: SELENOMETHIONINE (MSEat)
2au: SELENOMETHIONINE (MSEau)
2av: SELENOMETHIONINE (MSEav)
2aw: SELENOMETHIONINE (MSEaw)
2ax: SELENOMETHIONINE (MSEax)
2ay: SELENOMETHIONINE (MSEay)
2az: SELENOMETHIONINE (MSEaz)
2b: SELENOMETHIONINE (MSEb)
2ba: SELENOMETHIONINE (MSEba)
2bb: SELENOMETHIONINE (MSEbb)
2bc: SELENOMETHIONINE (MSEbc)
2bd: SELENOMETHIONINE (MSEbd)
2be: SELENOMETHIONINE (MSEbe)
2bf: SELENOMETHIONINE (MSEbf)
2bg: SELENOMETHIONINE (MSEbg)
2bh: SELENOMETHIONINE (MSEbh)
2bi: SELENOMETHIONINE (MSEbi)
2bj: SELENOMETHIONINE (MSEbj)
2bk: SELENOMETHIONINE (MSEbk)
2bl: SELENOMETHIONINE (MSEbl)
2bm: SELENOMETHIONINE (MSEbm)
2bn: SELENOMETHIONINE (MSEbn)
2bo: SELENOMETHIONINE (MSEbo)
2bp: SELENOMETHIONINE (MSEbp)
2bq: SELENOMETHIONINE (MSEbq)
2br: SELENOMETHIONINE (MSEbr)
2bs: SELENOMETHIONINE (MSEbs)
2bt: SELENOMETHIONINE (MSEbt)
2bu: SELENOMETHIONINE (MSEbu)
2bv: SELENOMETHIONINE (MSEbv)
2bw: SELENOMETHIONINE (MSEbw)
2bx: SELENOMETHIONINE (MSEbx)
2by: SELENOMETHIONINE (MSEby)
2bz: SELENOMETHIONINE (MSEbz)
2c: SELENOMETHIONINE (MSEc)
2ca: SELENOMETHIONINE (MSEca)
2cb: SELENOMETHIONINE (MSEcb)
2cc: SELENOMETHIONINE (MSEcc)
2cd: SELENOMETHIONINE (MSEcd)
2ce: SELENOMETHIONINE (MSEce)
2cf: SELENOMETHIONINE (MSEcf)
2cg: SELENOMETHIONINE (MSEcg)
2ch: SELENOMETHIONINE (MSEch)
2ci: SELENOMETHIONINE (MSEci)
2cj: SELENOMETHIONINE (MSEcj)
2ck: SELENOMETHIONINE (MSEck)
2cl: SELENOMETHIONINE (MSEcl)
2cm: SELENOMETHIONINE (MSEcm)
2cn: SELENOMETHIONINE (MSEcn)
2co: SELENOMETHIONINE (MSEco)
2cp: SELENOMETHIONINE (MSEcp)
2cq: SELENOMETHIONINE (MSEcq)
2cr: SELENOMETHIONINE (MSEcr)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
-1
Ligand/Ion
FE (III) ION
2
MSE
192
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(36, 36)
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)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:19 , GLU A:52 , HIS A:55 , FE A:902 , HOH A:909 , HOH A:910
BINDING SITE FOR RESIDUE FE A 901
02
AC2
SOFTWARE
GLU A:52 , GLU A:96 , GLU A:132 , FE A:901 , HOH A:910
BINDING SITE FOR RESIDUE FE A 902
03
AC3
SOFTWARE
GLU A:51 , GLU A:128 , GLU A:131 , GLU A:132 , HOH A:909 , HOH A:930
BINDING SITE FOR RESIDUE FE A 903
04
AC4
SOFTWARE
GLU B:19 , GLU B:52 , HIS B:55 , FE B:905
BINDING SITE FOR RESIDUE FE B 904
05
AC5
SOFTWARE
GLU B:52 , GLU B:96 , GLN B:129 , GLU B:132 , FE B:904
BINDING SITE FOR RESIDUE FE B 905
06
AC6
SOFTWARE
GLU B:51 , GLU B:128 , GLU B:131 , GLU B:132
BINDING SITE FOR RESIDUE FE B 906
07
AC7
SOFTWARE
GLU C:19 , GLU C:52 , HIS C:55 , FE C:908 , HOH C:922
BINDING SITE FOR RESIDUE FE C 907
08
AC8
SOFTWARE
GLU C:52 , GLU C:96 , GLU C:132 , FE C:907
BINDING SITE FOR RESIDUE FE C 908
09
AC9
SOFTWARE
GLU C:51 , GLU C:128 , GLU C:131 , GLU C:132 , HOH C:911
BINDING SITE FOR RESIDUE FE C 909
10
BC1
SOFTWARE
GLU D:19 , GLU D:52 , HIS D:55 , GLN D:129 , FE D:911 , HOH D:929
BINDING SITE FOR RESIDUE FE D 910
11
BC2
SOFTWARE
GLU D:52 , GLU D:96 , GLU D:132 , FE D:910
BINDING SITE FOR RESIDUE FE D 911
12
BC3
SOFTWARE
GLU D:51 , GLU D:128 , GLU D:131 , GLU D:132 , HOH D:914 , HOH D:915
BINDING SITE FOR RESIDUE FE D 912
13
BC4
SOFTWARE
GLU E:19 , GLU E:52 , HIS E:55 , FE E:914 , HOH E:925
BINDING SITE FOR RESIDUE FE E 913
14
BC5
SOFTWARE
GLU E:52 , GLU E:96 , GLU E:132 , FE E:913 , HOH E:925
BINDING SITE FOR RESIDUE FE E 914
15
BC6
SOFTWARE
GLU E:51 , GLU E:128 , GLU E:131 , GLU E:132 , HOH E:921 , HOH E:923
BINDING SITE FOR RESIDUE FE E 915
16
BC7
SOFTWARE
GLU F:19 , GLU F:52 , HIS F:55 , FE F:917 , HOH F:938
BINDING SITE FOR RESIDUE FE F 916
17
BC8
SOFTWARE
GLU F:52 , GLU F:96 , GLU F:132 , FE F:916
BINDING SITE FOR RESIDUE FE F 917
18
BC9
SOFTWARE
GLU F:51 , GLU F:128 , GLU F:131 , GLU F:132 , HOH F:924 , HOH F:939
BINDING SITE FOR RESIDUE FE F 918
19
CC1
SOFTWARE
GLU G:19 , GLU G:52 , HIS G:55 , FE G:920 , HOH G:940
BINDING SITE FOR RESIDUE FE G 919
20
CC2
SOFTWARE
GLU G:52 , GLU G:96 , GLU G:132 , FE G:919
BINDING SITE FOR RESIDUE FE G 920
21
CC3
SOFTWARE
GLU G:51 , GLU G:128 , GLU G:131 , GLU G:132 , HOH G:923 , HOH G:927
BINDING SITE FOR RESIDUE FE G 921
22
CC4
SOFTWARE
GLU H:19 , GLU H:52 , HIS H:55 , FE H:923
BINDING SITE FOR RESIDUE FE H 922
23
CC5
SOFTWARE
GLU H:52 , GLU H:96 , GLU H:132 , FE H:922
BINDING SITE FOR RESIDUE FE H 923
24
CC6
SOFTWARE
GLU H:51 , GLU H:128 , GLU H:131 , GLU H:132
BINDING SITE FOR RESIDUE FE H 924
25
CC7
SOFTWARE
GLU I:19 , GLU I:52 , HIS I:55 , FE I:926
BINDING SITE FOR RESIDUE FE I 925
26
CC8
SOFTWARE
GLU I:52 , GLU I:96 , GLU I:132 , FE I:925
BINDING SITE FOR RESIDUE FE I 926
27
CC9
SOFTWARE
GLU I:51 , GLU I:128 , GLU I:131 , GLU I:132
BINDING SITE FOR RESIDUE FE I 927
28
DC1
SOFTWARE
GLU J:19 , GLU J:52 , HIS J:55 , FE J:929
BINDING SITE FOR RESIDUE FE J 928
29
DC2
SOFTWARE
GLU J:52 , GLU J:96 , GLU J:132 , FE J:928
BINDING SITE FOR RESIDUE FE J 929
30
DC3
SOFTWARE
GLU J:51 , GLU J:128 , GLU J:131 , GLU J:132 , HOH J:940
BINDING SITE FOR RESIDUE FE J 930
31
DC4
SOFTWARE
GLU K:19 , GLU K:52 , HIS K:55 , FE K:932 , HOH K:961 , HOH K:998
BINDING SITE FOR RESIDUE FE K 931
32
DC5
SOFTWARE
GLU K:52 , GLU K:96 , GLU K:132 , FE K:931 , HOH K:998
BINDING SITE FOR RESIDUE FE K 932
33
DC6
SOFTWARE
GLU K:51 , GLU K:128 , GLU K:131 , GLU K:132 , HOH K:942 , HOH K:945
BINDING SITE FOR RESIDUE FE K 933
34
DC7
SOFTWARE
GLU L:19 , GLU L:52 , HIS L:55 , FE L:935 , HOH L:939
BINDING SITE FOR RESIDUE FE L 934
35
DC8
SOFTWARE
GLU L:52 , GLU L:96 , GLU L:132 , FE L:934
BINDING SITE FOR RESIDUE FE L 935
36
DC9
SOFTWARE
GLU L:51 , GLU L:128 , GLU L:131 , GLU L:132 , HOH L:1001
BINDING SITE FOR RESIDUE FE L 936
[
close Site info
]
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
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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_d1sq3a_ (A:)
1b: SCOP_d1sq3b_ (B:)
1c: SCOP_d1sq3k_ (K:)
1d: SCOP_d1sq3l_ (L:)
1e: SCOP_d1sq3c_ (C:)
1f: SCOP_d1sq3d_ (D:)
1g: SCOP_d1sq3e_ (E:)
1h: SCOP_d1sq3f_ (F:)
1i: SCOP_d1sq3g_ (G:)
1j: SCOP_d1sq3h_ (H:)
1k: SCOP_d1sq3i_ (I:)
1l: SCOP_d1sq3j_ (J:)
View:
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Folds
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Superfamilies
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
automated matches
(54)
Protein domain
:
automated matches
(54)
Archaeoglobus fulgidus [TaxId: 224325]
(1)
1a
d1sq3a_
A:
1b
d1sq3b_
B:
1c
d1sq3k_
K:
1d
d1sq3l_
L:
1e
d1sq3c_
C:
1f
d1sq3d_
D:
1g
d1sq3e_
E:
1h
d1sq3f_
F:
1i
d1sq3g_
G:
1j
d1sq3h_
H:
1k
d1sq3i_
I:
1l
d1sq3j_
J:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1sq3A00 (A:3-164)
1b: CATH_1sq3B00 (B:3-164)
1c: CATH_1sq3K00 (K:3-164)
1d: CATH_1sq3L00 (L:3-164)
1e: CATH_1sq3C00 (C:3-164)
1f: CATH_1sq3D00 (D:3-164)
1g: CATH_1sq3E00 (E:3-164)
1h: CATH_1sq3F00 (F:3-164)
1i: CATH_1sq3G00 (G:3-164)
1j: CATH_1sq3H00 (H:3-164)
1k: CATH_1sq3I00 (I:3-164)
1l: CATH_1sq3J00 (J:3-164)
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Architectures
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Topologies
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(
)
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)
Archaeoglobus fulgidus dsm 4304. Organism_taxid: 224325. Strain: dsm 4304.
(1)
1a
1sq3A00
A:3-164
1b
1sq3B00
B:3-164
1c
1sq3K00
K:3-164
1d
1sq3L00
L:3-164
1e
1sq3C00
C:3-164
1f
1sq3D00
D:3-164
1g
1sq3E00
E:3-164
1h
1sq3F00
F:3-164
1i
1sq3G00
G:3-164
1j
1sq3H00
H:3-164
1k
1sq3I00
I:3-164
1l
1sq3J00
J:3-164
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Ferritin_1sq3L01 (L:9-146)
1b: PFAM_Ferritin_1sq3L02 (L:9-146)
1c: PFAM_Ferritin_1sq3L03 (L:9-146)
1d: PFAM_Ferritin_1sq3L04 (L:9-146)
1e: PFAM_Ferritin_1sq3L05 (L:9-146)
1f: PFAM_Ferritin_1sq3L06 (L:9-146)
1g: PFAM_Ferritin_1sq3L07 (L:9-146)
1h: PFAM_Ferritin_1sq3L08 (L:9-146)
1i: PFAM_Ferritin_1sq3L09 (L:9-146)
1j: PFAM_Ferritin_1sq3L10 (L:9-146)
1k: PFAM_Ferritin_1sq3L11 (L:9-146)
1l: PFAM_Ferritin_1sq3L12 (L:9-146)
View:
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
(2)
1a
Ferritin-1sq3L01
L:9-146
1b
Ferritin-1sq3L02
L:9-146
1c
Ferritin-1sq3L03
L:9-146
1d
Ferritin-1sq3L04
L:9-146
1e
Ferritin-1sq3L05
L:9-146
1f
Ferritin-1sq3L06
L:9-146
1g
Ferritin-1sq3L07
L:9-146
1h
Ferritin-1sq3L08
L:9-146
1i
Ferritin-1sq3L09
L:9-146
1j
Ferritin-1sq3L10
L:9-146
1k
Ferritin-1sq3L11
L:9-146
1l
Ferritin-1sq3L12
L:9-146
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
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Solvent
All Atoms
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Protein & NOT Site
Protein & NOT PROSITE
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Chain C
Chain D
Chain E
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Chain G
Chain H
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Chain J
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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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Log
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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