PDB to Model¶

The user is able to retrieve pdb models from the Protein Data Bank and generate a 3D density volume from the atomic model.

General Workflow:¶

To launch:

1. The user enters the PDB ID (and check on the "use biological unit" check box if desired)
2. The user decides the resolution of the density model (typically filter to 15 - 25 Angstrom resolution)
3. The user selects the symmetry of the model
4. The user selects the pixel size for the model
5. The user selects the box size. Note: the user needs to make sure that the box size is sufficiently large to accommodate the 3D volume to be generated.

Output:

1. Once the model is generated, it will be deposited under "3d Density Volumes"
2. The user then assess the quality of the model and decides whether to convert the volume into an initial model

Notes, Comments, and Suggestions:¶