Dear yangzhanglab, I ran two proteins through Spring and Query B included the sequence VCSNPNCR the models were returned and on Model No.1 Query B has the sequence: VCSNCR with two amino acids missing. I could not find them within the predicted structure. The numbering of the amino acids was also not consistent with the the input sequence. I was expecting that N and C-terminal sequences that are not in the structure might not be shown but are internal residues that are not fitting the model removed? This is a critical region for me. The SPRING email printed sequence above the models is correct. In viewing in Pymol the residues are missing in the printed sequence at the bar along the top.
Thanks for any help.