Help

Note: the color bars in following pictures are addedd for illustration purpose

A. Saving and loading the pymol session

1. Click on "Downloads" on the right side of the screen.

2. Navigate to the desired file e.g. PSE for conservation & discriminants, and click on the "download" link.
3. Click to open the file in PyMOL directly. Alternatively, you can use the File -> Open on the Menu-Bar. You can use this method to open multiple files to the same PyMOL window.

B. Viewing the protein sequence:

1. You may also view the sequence of the peptides of the chains included in the strucutre file.

To do this, click on the "Sequence" option under the "Display" Menu-Bar.

Fig 1. Displaying the protein sequence



C. Interpreting the strucutre:

1. Click on the "conservation" tab.
2. This will then display the colours of the corresponding regions of the structure showing the conservation across all groups in the alignment.

Fig 2. Displaying the conservation regions across all groups



3. Unclick the "conservation" tab, and click on the "specificity" tab.
4. This will then display the colours of the corresponding regions of the structure showing the positions that are "conserved but different" (specific) across all groups.

Fig 3. Displaying the specificity regions across all groups



Fig 4. Displaying the conservation regions for the determinants in a particular group



Fig 5. Displaying the specificity regions for the determinants in a particular group