Viewer | SynGAP Server

Description of table metrics (columns)

Mol* mouse controls in the viewer

Rotate: click the left mouse button and move. Alternatively, use the Shift button + left mouse button and drag to rotate the canvas.
Translate: click the right mouse button and move. Alternatively, use the Control button + the left mouse button and move. On a touchscreen device, use a two-finger drag.
Zoom: use the mouse wheel. On a touchpad, use a two-finger drag. On a touchscreen device, pinch two fingers.
Center and zoom: use the right mouse button to click onto the part of the structure you wish to focus on.
Clip: use the Shift button + the mouse wheel to change the clipping planes. On a touchpad, use the Shift button + a two-finger drag.

More on Mol* page

3DViewer can be used to visualize molecular dynamics (MD) simulation trajectory snapshots of the modelled SynGAP missense variants. The user can move between three 150 ns replica simulations (˅) and between five models (><), including the initial variant model and MD simulations snapshots for 0 ns, 50 ns, 100 ns and 150 ns.

The table section provides additional information for each variant, including a detailed description of the structural effects of the missense mutation, structural annotation, relevant MD simulation metrics (e.g., RMSD, B-factor) and data plots (e.g., Ramachandran, RMSD), and sequence- and physics-based predictions (e.g., SIFT, PolyPhen-2) and official ClinVar status. Currently, structural modelling is provided for SynGAP missense variants that have a template within the scope of SynGAP model (residues from 198 to 730). Color of table rows is based on value of SGM Consensus.

Variant

Simulation