Get PDB File Dialog Box

This dialog box allows you to obtain proteins from either the PDB web site or a local copy of the PDB database and import them into Maestro. PDB structures are converted to Maestro format and can be colored according to structural issues (see Coloring Atoms, coloring set by a preference). Both PDB and mmCIF files can be downloaded. Map data can be downloaded for X-ray structures and cryo-EM structures.

If the import is successful, a banner is displayed in the Workspace. The banner offers a Prepare link to prepare the structure with the Protein Preparation Workflow Panel.

If you plan to use the structures for modeling, you should prepare them with the Protein Preparation Workflow beforehand. The Protein Preparation Workflow Panel also has a facility for obtaining a protein structure from a local database or the web site.

To open this dialog box, do one of the following:

  • Click the Tasks button and browse to Protein Preparation and Refinement → Get PDB Structure
  • In the Maestro main window, choose File → Get PDB
  • In the Project Table panel, choose File → Get PDB
  • Features
  • Additional Resources

Get PDB File Dialog Box Features

PDB IDs text box

Enter one or more 4-character PDB codes into this text box for the desired proteins, separated by commas or spaces (or both). You can use upper case or lower case for the code.

Chain name text box

If you only want to import a single chain from each protein, enter the chain name in this text box. To extract the chain with a blank name, use " ". This text box is disabled when downloading the biological unit, which contains all chains. The entire protein is downloaded, then the chain extracted into a separate file with the chain name as a suffix, e.g. 1fjs_A.pdb. If you entered more than one PDB code, the specified chain is extracted from each protein and imported (if it exists).

Include options

Select options for additional information to download.

  • Diffraction data/EM map—include the diffraction (reflection) data with the structure download, or the cryo-EM data. An information box opens on download, showing the name of the reflection data file. When the download finishes, the Map Type dialog box opens, so you can specify the type of map (surface) that was downloaded with the data. The choices include the common diffraction maps such as Fo-Fc, as well as Cryo-EM. Note: When this option is enabled, the PDB Dialog Box will generate the maps from structure factors for X-ray crystallographic structures, and will import the surfaces into Maestro.
  • Biological unit—download the entire biological unit rather than just the asymmetric unit (the default). This option is disabled when the source is Local Installation Only, as the biological unit can only be downloaded from the RCSB web site.
Fetching from text and Change button

This text reports the sources used to fetch the PDB file. Click the Change button to change the source, to one of the following options:

  • Local or Web—Retrieve the protein structure from a local copy of the PDB database, and if that fails, download the protein structure from the RCSB web site.
  • Local Installation Only—Retrieve the protein structure from a local copy of the PDB database. This option is incompatible with download of the biological unit.
  • Web Only—Download the protein structure from the RCSB web site.

The possible locations for the local copy of the PDB database are specified by environment variables. The structure is retrieved from the first location in the following list that has a valid PDB database:

  • $SCHRODINGER_PDB
  • $SCHRODINGER_THIRDPARTY/database/pdb
  • $SCHRODINGER/thirdparty/database/pdb
Download and Stop buttons

Clicking Download will start the download process and will display a progress dialog for the automatic map generation task. On this dialog, clicking the Stop button will cancel the task.

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