Hello
A colleague and I are working through the output of mkdssp and we have noticed some discrepancies (?) with it. Instead of a "software-error" it might simply be lack of experience on our part in which case, I would appreciate any further pointers to more information.
The "discrepancies" are as follows:
We have noticed that the number of H bonds reported in the header is not consistent with the energies reported in the table below the header. Would it be possible to clarify this point?
For example, considering PDB:8FAB, if we add up all the different bonds reported in the header, that would give a total of 1103. If we then go through the detailed bond breakdown and count all bonds whose index is non-zero, we find 848. (That is, go through the list of bond records, look across the indices of all 4 possible bonds and count 1 for any index that is non-zero).
We also noticed that the precision of the energies is kept to 1 decimal figure. What is the reason for this?
And finally we noticed that DSSP is not reporting side chains. Why are these not there? Is there anything we can do to model them?
All the best
P.S (01/11/19): Any help still appreciated :)
