TransAtlas:

TransAtlas Visualization Tab

TransAtlas visualization tab offers an interactive representation of the conformational transition thanks to the JSMol web viewer. A reduced trajectory with 100 representative snapshots chosen along the entire raw trajectory is shown in the JSMol window. The visualizer is coupled to three of the most important analysis done in TransAtlas:

• Collective Variables
• Moving Parts
• Residue Contacts (Broken, Formed, Transient)

Downloading of the reduced trajectory (in ASCII CRD format) represented in the window is also posible through a Download Trajectory Button in the JSMol panel.

Collective Variables

The set of Collective Variables (CVs) found for the particular conformational transition is shown in a table that is connected to the JSMol visualizer. Each of the CVs are identified by two residues (Cα). Collective Variables represent distances that best explain the RMSd change observed in the trajectory. The protocol used in TransAtlas guarantees that at least 95% of structural variance is captured by this set of CVs.

When clicking in one of the Collective Variables, the residues listed will be automaticaly represented in the visualization window as red spheres (Van Der Waals style), connected by a dashed line showing the distance between them in Angstroms.

Moving Parts

The set of Moving Parts found for the particular conformational transition is shown in a table that is connected to the JSMol visualizer. The table lists the identified moving parts, together with their size in number of residues.

When clicking in one of the Moving Parts, the molecule representation will be automaticaly changed in the visualization window, highlighting the residues belonging to the particular moving part in red colour and ball & stick style, whereas the rest of the protein will be shown in green colour and lines style.

Note here that the boundary between two moving parts locates residues playing a major role in protein flexibility, being hinge points a subset of them.

Residue Contacts

The set of Residue Contacts found for the particular conformational transition is shown in a table that is connected to the JSMol visualizer. The table groups the identified residues involved in broken, formed or transient contacts, and list them together with their size in number of residues.

Residue contacts observable identifies changes in the local environment of residues along the conformational transition leading to contacts forming and/or breaking either in transient or stable states.

Formed contacts are defined as those present (<7.5Å) at the last snapshot, but not observed (>12.5Å) in the initial structure. Broken contacts are defined as those present (<7.5Å) in the initial structure but not present (>12.5Å) in the final snapshot. Transient contacts are defined as those observed (<7.5Å) along the trajectory but neither in the initial structure nor in the final snapshot (>12.5Å). When clicking in one of the Residue Contacts group, the residues from the particular group will be automaticaly represented in the visualization window as red coloured ball & stick style, so that formed / broken / transient contacts could be easily tracked while the conformational transition is shown in JSMol.