ICM GUI Manual

[ Load PDB | Chemical Substructure | Query Sequence | PDB Field | Load NMR | Hyperlinks to Databases | Header ]

There are three main ways to read in a PDB file.

  1. Using the command line.
  2. Using File/Open button
  3. Using the PDB Search tab

Other PDB search options are described in more detail in the PDB Search section of this manual.

4.2.1 How to load a PDB Structure

There are three main ways to read in a PDB file.

  1. Using File/Open button
  2. Using the PDB Search tab
  3. Using the command line.

How to Search the Protein Databank and Download

The PDB search tab provides easy access to the PDB database. You can use keyword searching or type in the PDB code you are interested in. An asterisk (*) wildcard can be used to list all the pdb files currently available in the protein databank. Different fields can be searched by using the drop down arrow as shown below. More advanced PDB search tools and how to use the PDB search result table are described in the section entitled Searching the PDB.

Once a search is complete a table of PDB files relating to your search query will be displayed. To view the PDB file in 3D in the graphical display double click on a row in the PDBSearchResults table.

To Search the PDB and Download a Structure:
  • Click on the search tab and enter a search string or PDB code.
  • A table containing the results will be displayed.
  • Double click on a row to load the PDB file. Read more about PDB search here.

NOTE: If you have a PDB structure already saved you can read it into ICM by going to the File Menu and selecting Open. PDB files that have been viewed previously can be loaded using File/ Recent PDB Codes.

4.2.2 How to Search the Protein Databank by Chemical Substructure

Step 1: Click on the molecule editor button inside the search tab. Sketch the substructure you are interested in.

Step 2: A table containing the results will be displayed. Double click on a row to load the PDB file.

4.2.3 How to Query the PDB by Sequence

There are a number of ways to search the PDB by sequences.

  1. BLAST search the NCBI datase using the option "Sequences from PDB".
  2. Search by Sequence Pattern using the option in the Edit menu.
  3. Search by Identity using the option in the Edit menu.
  4. Search by Homology using the option in the Edit menu.

4.2.4 How to Query PDB by PDB Field

To query the PDB by field (Author, Compound, PDB Header, Experiment Type, Resolution or Ligand Code

4.2.5 Load and Display NMR Structures

Use the PDB Search tab to load NMR structures from the PDB. You can use the drop down button shown below to determine how you want to display your NMR structure. You can choose to display and download the first NMR model, all models in the PDB file or all models in the PDB in a stack. If you choose the stack option the the stack will be stored in the object as described here.

4.2.6 Hyperlinks to PDB Website and UniProt

In the PDB Search Results Table you will see blue hyperlinks that will take you directly to the PDB website or Uniprot website.

4.2.7 Display PDB Header

To display the PDB Header for a PDB file.