Exporting a PDB file from user-specified selections

As you walk through this tutorial, you will notice you are creating many new images, by highlighting various portions of the aligned protein sequences. If you would like to study this further, you can generate your own PDB file. To begin this process:

1 Highlight the portions of the sequence that you want to be selected in the Sequence Display of the main MultiSeq window.

2 In the main MultiSeq 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 MultiSeq 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 or equal to, and 0.0. Then click on the Select button in the Q Value window. The four sets of sequences will be highlighted. Click on Highlight PDB in the main MultiSeq window and 4 PDB files will be generated.

 

Figure 24: Where the generated PDB files will appear.

Generated files:
1asza2.0.pdb
1b8aa2.0.pdb
1efwa3.0.pdb
1sera2.0.pdb

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