Aligning in PyMol
PDB ID 1h9t contains a structure of both a DNA and a protein. It starts as one object.
Before we perform an alignment, we need to separate your DNA from the protein.
- Show sequence (click the S at the bottom right).
- Highlight all the "residues" from the chains X and Y (these chains contain each strand of your DNA) in the sequence bar at the top.
- Use the GUI to extract selection to new object (it's a faff doing this by terminal I find).
- Rename new object (automatically named obj01 probably) to DNA1, or whatever you prefer.
- Load your new, unaligned piece of DNA (I used
Pymol uses the CEalign algorithm to align structures in 3D space. You can call it using the following command:
cealign DNA1, 1BNA, object=aln
Another 3D alignment software I really like is the Dali server.
Haddock doesn't care if two molecules are aligned pre-analysis assuming you are submitting each DNA separately alongside a protein for binding analysis. This is because it tries a huge variety of orientations. Here is a list of things that you do need to do to your pdb before submitting to HADDOCK