[modeller_usage] How to (partially) override model.patch_ss_templates() ?

[Luca Jovine <>]

Hello,

I am trying to make a model of a disulfide-bonded protein, where some disulfides are the same as in my templates, but some are shuffled. I redefined the shuffled disulfides as described here:

https://salilab.org/modeller/9v7/examples/automodel/model-disulfide.py

but the models that I get always show the same exact disulfide connectivity of the templates, i.e. redefining special_patches does not seem to override model.patch_ss_templates().

Is there a way to achieve this, so that I can keep some conserved disulfides from my templates but change others?

Thanks,

Luca

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Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Member
Karolinska Institutet
Department of Biosciences and Nutrition & Center for Innovative Medicine
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
" class="">E-mail:
W3: http://jovinelab.org
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