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Molecular viewer support

In PDBj web site, we provide various molecular viewer pages. The available viewers for each web service is described below.

Services Molecular Viewer
jV Molmil Jmol JSmol
PDBj Mine (PDB data browser) asymmetric unit
PDBj Mine (PDB data browser) biological unit -
Chemie (chemical component browser)
EDMap (Electron Density Map)
Sequence Navigator / Structure Navigator
Promode Elastic
eF-site
Molecule of the Month

Others

  • Note that the actual performance will vary depending on the molecular viewer, web browser and system specifications.
  • Due to a recent revision of the Google Chrome web browser, the outdated plugin system used by Java is no longer supported and thus Java no longer works within Chrome. So molecular viewer pages with jV and Jmol are not available on Chrome. Chrome users are advised to either use Molmil/jsmol or switch to an alternative browser like Firefox which does support the outdated plugin system.
  • In case Java could not be detected, no links to jV and Jmol will be shown. To test whether you have Java installed and enabled, please visit our browser support test page to test whether your browser supports Java.
  • The Jmol page doesn't support Mac OS 10.6. Please refer another molecular viewer page such as JSmol page.

Mine Asymmetric Unit

  • Static images:
    • The images were created using Molmil.
  • Available viewers:
    • jV and Jmol are available on systems supporting Java Runtime Environment (JRE) when the molecular weight of the structure is less than 1.25MD. On non-mobile systems, such as iOS and Android, these viewers are not available because they don't have support for Java applets.
    • Molmil is available on systems which support webGL and the (compressed) PDBx/mmCIF file is less than 20MB. On 64 bits browsers (excluding Chrome due to limitations of Chrome's JavaScript engine), the limit is higher at 100MB. Note that to load this type of large structures, a huge amount of memory is required (> 8GB).
    • JSmol is only available when the (compressed) PDBx/mmCIF filesize is less than 1MB due to performance reasons.

Mine Biological Unit

  • Static images:
    • The images were created using Molmil.
    • Molmil's coarse surface was inspired by UCSF Chimera's Multiscale model*1).
  • Available viewers are jV and Molmil. System requirements about jV and Molmil are same as Mine Asymmetric unit.

*1) Software extensions to UCSF chimera for interactive visualization of large molecular assemblies.
Goddard, T.D., Huang, C.C., Ferrin, T.E. Structure 13: 473-482 (2005) [doi:10.1016/j.str.2005.01.006]

2014-08-21 (last edited: 4 months ago)2016-11-18
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