Exporting File Formats

Exporting a PDB file from user-specified selections

As you walk through this tutorial, notice many of the new images you've created in the OpenGL Display. Often these images are generated by highlighting specific portions of the aligned protein sequences. If you would like to study your selections further, you can can do so by generating your own PDB file(s). To begin this process:

1

Highlight the portions of the sequence that you want to examine in the Sequence Display of the main Multiple Alignment window.

2

In the main Multiple Alignment window top pull-down menu, go to View $\rightarrow$ Highlight style. Multiple Highlight styles will appear to choose from. Select one and make sure it appears in the OpenGL Display.

3

Go back to the Multiple Alignment window and click on File $\rightarrow$ Write PDB from selection....

4

The PDB file(s) will be saved in a directory that can be chosen by clicking on the File $\rightarrow$ Choose Work Directory.... If you haven't selected your Work directory, you be prompted to choose a directory when you click on Write PDB from selection....

5

If you want to save the entire alignment, you can do so by going the Residue Selection and selecting Q Value, Greater than, and 0.0. Then click on the Select button in the Q Value window. The four sets of sequences will be highlighted. Go to File $\rightarrow$ Write PDB from selection... and four PDB files will be generated.

These molecules can then be loaded to VMD and Multiple Alignment for further analysis.

Exporting a multiple alignment in FASTA format

You can create a FASTA format file from the aligned molecules. To do this:

1

Go to the main Multiple Alignment window and select File $\rightarrow$ Write alignment in FASTA format.

2

A browser window should appear where you can save the file. Select where you want to save the FASTA file. You may also change the name of the file in the provided dialog.

3

Save the file by hitting either a Save or OK button, or by hitting the Enter/Return key.

Figure 24: FASTA menu

You also have the option of writing the secondary structure data into a FASTA file.
To do this:

4

Select File $\rightarrow$ Write FASTA file with secondary structure data.

5

A file browser window will appear. Select where you want to save the FASTA file. You also have the option of changing the file name in the browser window.

6

Click either the Save or OK button, or hit the Enter or Return key to save the FASTA files.

FASTA is a common alignment file, which enables you to study multiple alignments in many other applications.