Molstar viewer

[brindakv]

Molstar is a web application for visualizing structures of macromolecules. For an example visualization, see here.

We can incorporate Molstar in the PDB-Dev Deriva catalog so that users can visualize the structures directly.

The software is maintained in a public Git repository.

More information on embedding Molstar viewer: https://unpkg.com/browse/molstar@3.3.1/build/viewer/

Updated js, css and html files: https://github.com/informatics-isi-edu/protein-database/tree/master/scripts/molstar

[svoinea]

Additional files were needed:

• bootstrap4.1.3.min.css

• em-styles-cutdown.css

• navbar.css

• bootstrap3-typeahead.min.js

• bootstrap4.1.3.min.js

• jquery-3.3.1.min.js

• popper1.12.9.min.js

For example, in the file view3d.html, there is this line:

                $(document).ready(on_ready); 

The $ is defined in jquery. All those files I was able to download them from pdb-dev.wwpdb.org. However, there are still files missing. See:

Current view on dev.pdb-dev.org:

[brindakv]

Python-ihm version is 0.23 on both staging and production catalogs.

[brindakv]

The issue with Molstar is in the entity table. _entity.type is of type ucode. Since we capitalize all ucode data items, we have it as POLYMER. mmCIF rules allow it. But Molstar expects this to be lowercase polymer.

[brindakv]

@svoinea Molstar version 3.6.1 has a fix for this issue: https://unpkg.com/browse/molstar@3.6.1/build/viewer/

Please make sure to download the raw js and css files from the link above.

[brindakv]

Make image smaller; move visualization next to image; make visualization larger; update name to 3D Visualization

[svoinea]

Done on catalog 99 under the commit # 73d0c4f.

[brindakv]

Update molstar panel size to 800px x 700px

3D Visualization should be allowed for the following Workflow Status: mmCIF CREATED, SUBMISSION COMPLETE, HOLD, RELEASE READY, REL

Default text to be shown for the 3D Visualization column when the structure cannot be visualized (i.e., all other status than those mentioned above): 3D Visualization is available after a compliant mmCIF file is created

[svoinea]

Panel size was updated to 800px x 700px. 3D Visualization is allowed now for the following Workflow Status: mmCIF CREATED, SUBMISSION COMPLETE, HOLD, RELEASE READY, REL. For the rest of the Workflow Status the text Not Available is displayed.

Currently, it is available only on catalog 99.

[brindakv]

Looks good on dev. Can be moved to staging and production.

[svoinea]

Already moved to staging and production.