Is it possible to model only certain atom in the modeller using Model-ligand.py?

26 September 2021 1 6K Report

I have a generated a model based on a template. this template also contains a natural ligand, 4 calcium atoms, and a zinc. I would like to add the zinc and calcium atom but not the natural ligand. How is it possible to do it in MODELLER? thank you

Amjad Hasan Bazzari

Dear Caroline Jilbert

From the MODELLER manual in the following link (section 2.2, page 39):

https://salilab.org/modeller/9.21/manual.pdf

"If you have extra HETATM ligands in the template which you don’t want in the model, simply align them with a gap (’-’) in the model sequence."

I hope this helps

Good Luck

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