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 ------------------------------------------------------------------------ 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 E-mail: luca.jovine@ki.se<mailto:luca.jovine@ki.se> W3: http://jovinelab.org ------------------------------------------------------------------------ När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.