Molstack

Description

Molstack is a platform for sharing experimental maps and their interpretations that supports the visualization, analysis and validation of multiple sets of coordinates and density maps. It allows the interactive inspection of data through the simultaneous presentation of multiple datasets and models in a way that allows for easy pairwise comparison.

The platform allows users to create and share Molstack projects. The platform offers a “hands-off” approach, and users are allowed to combine any type of models and maps into individual stacks and define views as they see fit. This flexibility allows the Molstack platform to host projects that can be used for distinct purposes.

Examples of different use-cases

1. Presenting the experimental evidence, such as 2mF_o-DF_c maps, and an omit map for small molecule ligands and its surrounding.
2. Presenting alternative interpretations of the data such as re-refinement.
3. Sharing speculative modeling and interpretation of ambiguous data.
4. Collaboration

Definitions

Molstack uses several concepts and terminology defined below:

Molstack project

set of maps and models organized into groups that are displayed individually.

Viewport

A single window displaying one indvidual group of maps and models

Stack

Group of maps and models that are displayed in a single viewport. In each viewport, the user viewing the project can select one stack to be displayed and compare two stacks side-by-side.

Views

The projects can have defined views. Views allow the project creator to define coordinates accompanied by a description. The user viewing the project can jump between these predefined views. The description of the views form a narrative for the project

Molstack collection

Group of individual projects that can have its own description and is accessible using single identifier

Public project/collection

Project/collection that can be accessed using link. If the project/collection is not marked as public it is only accessible to the owner of the project. If public project is not searchable it can only shared using long type identifier

Searchable project/collection

Project/collection is displayed in the lists of the publicly accessible projects and collections. Consequently, the projects/collections that are public but not searchable are accessible only using the randomized link. It is necessary for projects to be searchable to be accessible using short mlstk_XXXX identifiers and short links.

Recognized formats

Currently, Molstack recognizes model files in the PDB format and maps in CCP4/MRC format. It can also generate maps from the amplitudes or anomalous differences and phases provided in the MTZ file. Molstack can download all models directly from the PDB. Download of the maps from the PDB is currently limited to crystallographic data. Maps are downloaded from the PDBe.

Limitations

Superposition

Molstack does not make superposition of models and maps by its own. All models and maps need to be superposed before upload. For the related crystallographic models and maps we recommend standardizing the unit cell placement within unit cell using Achesym

Large, high resolution maps

It may take a while to download and process high resolution maps that cover the large unit cells and/or have high symmetry. Its recommended that users creating projects check the performance using the preview feature. If the loading of the maps is unacceptably slow, it is recommended to cut and upload only relevant part of the map.