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EMDB-1422 Display options
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Processing surface dataLoading
Processing structure dataLoading
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-1422
DataLoading
AssemblyLoading
Total massLoading
AuthorsLoading
DateLoading
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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Group:

Keywords:
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no data
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
ZoomSmall
Large
%
SlabNear
Far
Scale
Save
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Style
This is the panel to control the style of the structure data.
Current modelEMDB-1422
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/1422/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:-

Help

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News

  • NEW! Now, Yorodumi supports Java-incompatible browsers including some tablet PCs and phones. Select JSmol or JSmol-GL as the viewer for such the browsers/devices.

Mouse operation

  • Jmol (details)
    Left buttonMiddle buttonRight button
    Jmol menuCtrl + Click Click
    X/Y rotationDrag
    X/Y moveShift + Double-click & DragDouble-click & DragCtrl + Drag
    Z rotationShift + horiz. Draghoriz. DragShift + horiz. Drag
    Zoom in/outShift + vert. Dragvert. Drag or Wheel rotation

Features of the viewers

ViewersEnvironment, etc.Functionality in YorodumiRecommended for...
JmolJava requiredFullRecommended if it works
JSmolJava NOT required (HTML5)Nearly full but slowRecommended if Java is unavailable (for mobile devices etc.)
JSmol-GLJava NOT required (HTML5, WebGL)LimitedMuch faster than JSmol on some devices
jVJava required, OpenGLNearly fullHigh performance and beautiful view by OpenGL
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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