Marcus,
it appears that coot "breaks" bonds when the distance between atoms
exceeds 1.64A pretty much irrespective of the bond type. Two exceptions
are, of course, sulfurs in MET/CYS. CB-SG bond in cysteine does not
seem to have any cutoff (when you do rotate/translate zone in coot, you
can move
Dear Marcus
The most likely reason is that geometry is a bit loose. You need to tighten it
a bit.
You can do by decreasing weight using weight matrix option on the interface.
You need also check the electron density to make sure that ILE is in electron
density.
Please let me know if you hav
Well - REFMAC and I think other refinement programs simply read in an
atom with occupancy 0.00 and write it out again in exactly the same
place.. All refinement contributions for atoms both Xray and geometrical
are weighted by the atom occupancy so such an atom will not shift.
The assumption i
Dear all,
I might excuse myself for the silly question but it is the first time I
solve an x-ray structure.
After modell building in coot and running of refmac with restrained
refinement I have the problem that the pdb output file contains
distances between e.g. ILE Cb and Cg that are so long tha
