There are two ways to search a sequence against the PDB database.

OPTION 1:

If your sequence is already loaded into ICM:

• Select Edit/PDB Search by sensitive similarity
• Type the sequence name into the Sequence name field. Sequences which are already loaded into ICM can be seen by clicking the drop-down button
• Select the number of hits you wish to see by typing the number into the Limit field. A number can also be selected by clicking on the up and down arrows. (Default is 50)
• Select the sensitivity of your search by typing a value into the Expect field. This value is a database-size error estimate and the default value is 0.01.
• Choose whether you wish to display All entries or Entries with unique sequence by checking the appropriate button.
• If you wish to load the sequences leave the Load Sequences box checked.
• If you merely want to see the PDB codes which are similar to your sequence then un-check the Load Sequences box.
• Click the OK button.

OPTION 2:

If your PDB sequence is not loaded into ICM:

• Select Edit/Search with external sequence
• Cut and paste or type (shown below) your sequence into the Sequence data entry field.
• Select the number of hits you wish to see by typing the number into the Limit field. A number can also be selected by clicking on the up and down arrows. (Default is 50)
• Select the sensitivity of your search by typing a value into the Expect field. This value is a database-size error estimate and the default value is 0.01.
• Choose whether you wish to display All entries or ** Entries with unique sequence ** by checking the appropriate button.
• If you wish to load the sequences leave the Load Sequences box checked.

NOTE: If you merely want to see the PDB codes which are similar to your sequence then un-check the Load Sequences box.

• Click the OK button.

NOTE: You can also use the toolbar search option by homology if you wish.