- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- PDB Format
- PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full PDF
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 2 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
- Biological Assembly 2 (PDB - gz)
Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution
NOTE: Use your mouse to access Jsmol features and to drag, rotate, and zoom in and out of the structure.Help
Jmol._Canvas2D (Jmol) "jmolApplet0"[x]
loadScript /js/jsmol/j2s/core/package.js
loadScript /js/jsmol/j2s/core/corejmol.z.js
loadScript /js/jsmol/j2s/J/translation/PO.js
loadScript /js/jsmol/j2s/core/corescript.z.js
JSmol exec jmolApplet0 start applet null
Jmol JavaScript applet jmolApplet0__437774262239566__ initializing
Jmol getValue debug null
Jmol getValue logLevel null
Jmol getValue allowjavascript true
AppletRegistry.checkIn(jmolApplet0__437774262239566__)
vwrOptions:
{ "name":"jmolApplet0","applet":true,"documentBase":"https://www.rcsb.org/3d-view/jsmol/1NKZ","platform":"J.awtjs2d.Platform","allowjavascript":true,"fullName":"jmolApplet0__437774262239566__","codePath":"https:/js/jsmol/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"437774262239566","bgcolor":"#FFFFFF" }
setting document base to "https://www.rcsb.org/3d-view/jsmol/1NKZ"
(C) 2015 Jmol Development
Jmol Version: 14.31.4 2020-09-06 18:16
java.vendor: Java2Script (HTML5)
java.version: 2019-06-08 00:17:46 (JSmol/j2s)
os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)
Access: ALL
memory: 0.0/0.0
processors available: 1
useCommandThread: false
appletId:jmolApplet0 (signed)
Jmol getValue emulate null
defaults = "Jmol"
Jmol getValue boxbgcolor null
Jmol getValue bgcolor #FFFFFF
backgroundColor = "#FFFFFF"
Jmol getValue ANIMFRAMECallback null
Jmol getValue APPLETREADYCallback Jmol._readyCallback
APPLETREADYCallback = "Jmol._readyCallback"
StatusManager callback set for APPLETREADYCallback f=Jmol._readyCallback cb=APPLETREADY
Jmol getValue ATOMMOVEDCallback null
Jmol getValue AUDIOCallback null
Jmol getValue CLICKCallback null
Jmol getValue DRAGDROPCallback null
Jmol getValue ECHOCallback null
Jmol getValue ERRORCallback null
Jmol getValue EVALCallback null
Jmol getValue HOVERCallback null
Jmol getValue IMAGECallback null
Jmol getValue LOADSTRUCTCallback null
Jmol getValue MEASURECallback null
Jmol getValue MESSAGECallback null
Jmol getValue MINIMIZATIONCallback null
Jmol getValue SERVICECallback null
Jmol getValue PICKCallback null
Jmol getValue RESIZECallback null
Jmol getValue SCRIPTCallback null
Jmol getValue SYNCCallback null
Jmol getValue STRUCTUREMODIFIEDCallback null
Jmol getValue doTranslate null
language=en_US
Jmol getValue popupMenu null
Jmol getValue script null
Jmol getValue loadInline null
Jmol getValue load null
Jmol applet jmolApplet0__437774262239566__ ready
script 1 started
antialiasDisplay = true
loadScript /js/jsmol/j2s/core/corescriptcmd.z.js
FileManager.getAtomSetCollectionFromFile(https://files.rcsb.org/download/1nkz.cif)
FileManager opening url https://files.rcsb.org/download/1nkz.cif
The Resolver thinks MMCif
loadScript /js/jsmol/j2s/J/adapter/readers/cif/MMCifReader.js
loadScript /js/jsmol/j2s/J/adapter/readers/cif/CifReader.js
loadScript /js/jsmol/j2s/JU/CifDataParser.js
loadScript /js/jsmol/j2s/core/corebio.z.js
filtering with ;BIOMOLECULE 1;
TITLE: The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 A resolution and 100K : new structural features and functionally relevant motions.
TITLE: Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria.
TITLE: Pigment-pigment interactions and energy transfer in the antenna complex of the photosynthetic bacterium Rps. acidophila.
TITLE: Apoprotein Structure in the LH2 complex from Rhodopseudomonas acidophila Strain 10050: Modular assembly and protein pigment interactions
BCL = BACTERIOCHLOROPHYLL A
BEN = BENZAMIDINE
BOG = octyl beta-D-glucopyranoside
CXM = N-CARBOXYMETHIONINE
HOH = WATER
RG1 = Rhodopin b-D-glucoside
Setting space group name to HM:H 3 2
biomolecule 1 operators 1,2,3 ASYM_IDs A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA
found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA
biomolecule 2 operators 1,2,3,4,5,6 ASYM_IDs A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA
found biomolecule 2: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA
assembly operator 1 x,y,z
assembly operator 2 -y,x-y,z
assembly operator 3 -x+y,-x,z
assembly operator 4 y,x,-z
assembly operator 5 x-y,-y,-z
assembly operator 6 -x,-x+y,-z
1NKZ
12 bonds added
loadScript /js/jsmol/j2s/core/coresym.z.js
Time for openFile(https://files.rcsb.org/download/1nkz.cif): 1968 ms
reading 10383 atoms
ModelSet: haveSymmetry:true haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
10383 atoms created
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Time for creating model: 235 ms
TITLE: The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 A resolution and 100K : new structural features and functionally relevant motions.
TITLE: Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria.
TITLE: Pigment-pigment interactions and energy transfer in the antenna complex of the photosynthetic bacterium Rps. acidophila.
TITLE: Apoprotein Structure in the LH2 complex from Rhodopseudomonas acidophila Strain 10050: Modular assembly and protein pigment interactions
BCL = BACTERIOCHLOROPHYLL A
BEN = BENZAMIDINE
BOG = octyl beta-D-glucopyranoside
CXM = N-CARBOXYMETHIONINE
HOH = WATER
RG1 = Rhodopin b-D-glucoside
found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA
found biomolecule 2: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA
1NKZ
12 bonds added
Script completed
Jmol script terminated
script 2 started
0 atoms hidden
10383 atoms selected
3159 atoms selected
0 atoms selected
0 atoms selected
0 atoms selected
10383 atoms selected
Script completed
Jmol script terminated
script 3 started
0 atoms hidden
10383 atoms selected
defaultColorScheme = "jmol"
3159 atoms selected
10383 atoms selected
Script completed
Jmol script terminated
script 4 started
Script completed
Jmol script terminated
loadScript /js/jsmol/j2s/J/g3d/HermiteRenderer.js
Scripting Options
Structure Details
Select Options
Surface options may take a long time to render, especially for larger structures
Select a different viewer
Help Links
Jmol, an open source Java viewer for chemical structures in 3D (http://www.jmol.org)
