Problem about Airviewer in Pymol

HADDOCK
1

I am new to docking and have been trying to reproduce the results of the Protein-DNA docking Using HADDOCK High-Ambiguity Driven DOCKing. The tutorial uses a pymol plugin to derive the Ambiguous Interaction Restraints (AIRs).
When I used that script I found that “self.pairSelect[1][‘selection’] = self.airstore.resolveSelection(quickselect=self.atomselector)”

So, I would like to know how to solve this problem ?

2

Hi Nott,

Thanks for the interest you have in running Haddock for protein-DNA complexes and following our tutorial.
First, I must emphasize that the advanced tutorial is still under construction and not fully revised and optimised.

Nevertheless, regarding you issue, I guess that you are trying to run the AIRviewer.py script in your terminal with python, which you should not do.
Indeed, this script is a PyMol module that should be run by PyMol only.
I have re-tried it this morning, and it was working as expected.
To properly function, you must:

  1. open a new pymol session

  2. go to the directory where the file airesession.pdb is present ( using the pymol python interpreter )

cd 3CRO/part_3

  1. Load the airseesion.pdb file ( using the pymol python interpreter )

load airsession.pdb

  1. Finally, run the AIRviewer.py PyMol module ( using the pymol python interpreter )

run …/tools/AIRviewer.py

  1. The remaining set of actions in the tutorial should go fine, just follow them.

I hope this answer will solve your problem.

Cheers, Victor

3

Hello,

Thank you for your answer.
I try to run on Pymol but I still found that problem as shown in attached files.

Screenshot 2023-11-22 171535
Screenshot 2023-11-22 1715351915×1006 112 KB

4

Thank for the feedback, trial and screenshot.
I can now understand the issue: it is related to the fact that the AIRviewer.py is still a python2 script.

I had to update the script to be python3 compatible and have created a new surfdrive link, which contain with the version of the scripts.

Please, download the new archive using this link (SURFdrive) and give it a try.

I hope it will solve your issue.

5

Thank you for your help !! The problem was solved :slight_smile:

However, I would like to know how to create “complex” for airsession in part 3 ?

6

Good to know you were able to generate AIR restraints file (ambig_pm.tbl) and reach the end of part 3.
Thanks for the feedback !

The complex will not be generated in part 3, that is devoted to the generation the AIR restraints file only.
The airsession file is a PyMol session enabling you to visualise the entities and use the AIRviewer.py to create the restaints file, that will be used for the later three-body protein-DNA docking.

The complex will be generated in the next part, using the Haddock2.4 webserver, where you will first input the pdb files and then the restraints file you just created.