Question about vizualization of docking protein-DNA (2.4 tutorial / own data)

[ldrahnik]

Hello,

I am interested in generating the same image as is https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-protein-DNA-advanced/PyMol.jpg so I would like to generate the same image according to tutorial first, then generate image for my own transcriptional factor docking DNA. I use Haddock3 and I already run Haddock3 for my own protein/dna sequence so I have some .pdbs on output. At first in an advanced tutorial for Haddock2.4 /education/HADDOCK24/HADDOCK24-protein-DNA-advanced/ I found a PyMol plugin named ../tools/AIRviewer.py so I jumped directly to heading Using the PyMol plugin to create the AIR file (I hope I could skip first parts of tutorial), I tried to download fixed tool for Python3 from link in this topic Problem about Airviewer in Pymol (I had to add r because python3 in row 801: splitter1 = re.compile(r'\(|\)'); startassign = False) and run commands according to the tutorial and attached screenshot but after that, output does not look like the same as in tutorial. I also had to move to the folder 3CR0/part_3 file ambig_pm.tbl taken in sibling folder part_3-arch. It was not mentioned in that part of tutorial so I guess the tutorial is one chain?

Thank you

[AKravchenko]

Hi there,

To achieve such visuals, one does not need AIRviewer. It can be achieved simply by showing molecules as surface and setting transparency value accordingly.

To recreate the image you linked, first colour the chains in your favourite colours, then:
show cartoon
set cartoon_ring_finder, 3
show surface
set transparency, 0.5

[AKravchenko]

As for the AIRviewer, it can display AIRs, etc., like so:

Latest version is available here