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EMDB-5294
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Java Runtime Environment (JRE) is necessary to use the molecular viewer.
These are the buttons to show the corresponging panels. You can move, resize, and hide the panels by the mouse.
Data
In this panel, some brief descriptions about the current data entry are shown.
The structure data in the viewer may be modified to reduce its data size.
Database-IDEMDB-5294
DataLoading
AssemblyLoading
Total massLoading
AuthorsLoading
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Open
This panel is used to open the other data entry within Yorodumi (this web site).
Input ID
PDB ID / EMDB ID / ChemComp ID:
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Keywords:
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View
This is the panel to control the manner of whole the viewer, such as the viewing orientation and the zoom level, etc. To control the style of the strucuture data, use the Style panel.
Viewer  Background: Depth Cueing- Stereo-
Orientation
OrientationRotation
Center
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%
SlabNear
Far
Scale
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Style
This is the panel to control the style of the structure data.
Current modelEMDB-5294
Surface style
Color
TransparencyOpaque
clear
Command
In this panel, the histories of the command lines sent from Yorodumi to Jmol are shown.
$ set ambientPercent 20; set diffusePercent 70;set specular ON; set specularPower 80; set specularExponent 5;set specularPercent 70;set antialiasDisplay ON; set antialiasTranslucent ON;set ribbonBorder ON;set PickCallback "_mousepick";set MessageCallback "_jmolmsg";set languageTranslation OFF;set chainCaseSensitive TRUE; isosurface s1 file "http://pdbj.org/emnavi/data/emdb/media/5294/ym/o1.zip|o1.jvxl"; isosurface s1 OPAQUE [X77ee77]; slab off; set zshade on; set zshadepower 1; set zslab 60;set echo bottom left;font echo 18 serif bold; color echo blue;
Command:

Current selection: all -> 0 atoms

Mouse picking: Chain:- Residue:- Atom:-

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Schemes

Small molecules

[All] Ball&Stick model, CPK color

[All] CPK model, CPK color

Ordinary proteins

[Protein/RNA/DNA] cartoon model, rainbow color by monomer / [Hetero atoms] 50%CPK model, CPK color

[Protein/RNA/DNA] backbone model, color by structure / [Hetero atoms] 50%CPK model, CPK color

Large complexes

[Protein/RNA/DNA] backbone model, color by chain / [Hetero atoms] CPK model, CPK color

[Protein] rocket model, color by chain / [DNA/RNA] chain-trace model, color by chain / [Hetero atoms] CPK model, CPK color

[All] CPK model / [Protein/RNA/DNA] color by chain / [Hetero atoms] CPK color

Select

Click selection
Display
Atom style
Chain style
Color


Rainbow:
others:
TransparencyOpaque
clear
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Styles are applied only to current "selected" elements