Hi,
I would like to use ColabDesign's AF module as part of a larger pipeline. At one step in the pipeline I only need to predict the protein structure from a sequence that I got from a previous step. However, the plain structure prediction by using "bbfix" is not really good and I want to use a template for the prediction. However, to give Alphafold has little information as possible I would like to provide only a partial template. So far I generated a backbone-only PDB of my target structure and replace the residue names by GLY. However, I struggle right now to correctly use the partial mode (I assume that this is the correct way to use this mode). More specific, what should I provide for the pos argument is it the part of the protein I want to use as a template or is this the part of the protein for which I do not want to use the template for?
Thank you very much!
Best,
Marius
Hi,
I would like to use ColabDesign's AF module as part of a larger pipeline. At one step in the pipeline I only need to predict the protein structure from a sequence that I got from a previous step. However, the plain structure prediction by using "bbfix" is not really good and I want to use a template for the prediction. However, to give Alphafold has little information as possible I would like to provide only a partial template. So far I generated a backbone-only PDB of my target structure and replace the residue names by GLY. However, I struggle right now to correctly use the partial mode (I assume that this is the correct way to use this mode). More specific, what should I provide for the
posargument is it the part of the protein I want to use as a template or is this the part of the protein for which I do not want to use the template for?Thank you very much!
Best,
Marius