Error running build_seq.py

HADDOCK
1

Hi
I am not sure this is the right place to ask, if not please let me know who I can ask.
I am trying to run a script that is used in HADDOCK papers (Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK) called “build_seq.py” in pymol and I am encountering the following error:

PyMOL>run build_seq.py
PyMOL>build_seq peptide, QGAADLESLGQ, phi=-60, psi=-40
Building sequence: QGAADLESLGQ
Error: Selection 0: Invalid selection name “_tmp_editor”.
( _tmp_editor and name N )<–
and only the first 4 amino acids are built.

I changed the code to work with Python 3 since I have a newer version of Pymol (changed the print and except syntax)
I’ll really appreciate your help.
Best,
Miriam

2

It is a python version problem I am afraid…

Last time we used it on the nmrbox VMs and it worked fine.

3

hi,

I tried to convert the script to a python3-compatible version, it is working on my machine (pymol 2.5.5, macbook air M1), check it out build_seq_3.py.txt (6.8 KB) and let me know if it works!

you’ll have to rename it to build_seq_3.py first

Best,
Marco

4

Thank you!
Unfortunately, it does not work on my laptop (Windows) Pymol version 2.5.5. It builds only part of the peptide.

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