I am using a custom method to predict HELIX/SHEETs for proteins and want to compare my results with what is stored in the PDB file.
For this I compare the coordinates of both methods. The problem I run into is that PDB files frequently start with a coordinate != 1 (e.g. 3LX3.pdb with 669) while my data always starts with 1.
Is there an easy way to get the offset between the two files ? I was thinking of doing a alignment of both sequences but was wondering if there is an easier way ?
Thanks in advance...