Is there any way to force Modeller to generate restraints for
consecutive CA atoms instead for every other one? What is the reason for
excluding i, i+1 restraints for CA atoms?
The i, i+1 CA-CA restraint (also the N-O and sidechain-sidechain
restraint) is excluded because it would conflict with the stereochemical
backbone restraints, but you can certainly turn it back on. Just modify
or override the mkhomcsr method in the automodel class
(modlib/modeller/automodel/automodel.py). The ranges for all three of
these restraint types are currently set to (2, 99999). Just change them
to (1, 99999).