Hello Everyone,
I'm trying to model the structure of a chimeric protein composed of three known structures in the PDB.
However when I run the modelling process using one of these known structures as a constraint, but without alignment, the predicted structure it produces I know is incorrect because the template structure does not appear in the final model as it should (it is a trans-membrane 4 helical bundle).
I need help generating the .txt file containing the fasta sequence alignment plus PDB information (option 1 specify template with alignment) however I am not an advanced user and so far have had no success creating this detailed file to constrain my model. I have tried Blastp but cannot get it to output a useful FASTA text file, and I cannot extract the coordinate information from my PDB files either.
Any help or useful web links would be appreciated.
All the best,
Joe