Hello,
I am refining structures with the modified individual B-factor refinement
at 1.8A resolution on xplor3.851.
lines:
REMARKS file bref_tnt.restr
REMARKS contains Dale Tronrud's parameters for atomic temperature factor
REMARKS refinement (published in J. Appl. Cryst. 29, 100-104 (1996) )
REMARKS for main chain atoms, 898 examples
bsigma = ( name N or name CA ) = 4.6
bsigma = ( name CA or name C ) = 7.4
bsigma = ( name C or name N ) = 6.6
bsigma = ( name C or name O or name OT* ) = 6.3
REMARKS alanine side chains, 80 examples
bsigma = ( resnam ALA and ( name CA or name CB ) ) = 3.5
REMARKS arginine side chains, 36 examples
bsigma = ( resnam ARG and ( name CA or name CB ) ) = 8.5
bsigma = ( resnam ARG and ( name CB or name CG ) ) = 16.5
..
REMARKS no weights on angles
asigma = ( not name H* ) = 1000000
I have checked the log file and there are 98 bond_B_restraints groups and
the number and rmsd in statistics for each group are incorrect. It shows
that the above script doesn't work. I guess that the group number for
atom is considered only by the final evaluation and a few bond restraints
for the pair atoms with same group number are selected under the assigned
sigma_bonds. There is also a same question that in the case of the
original brefinement.inp script, what is the sigma_bonds for CA-CB bonds
which must be assigned with the different group number. (it must be
default)
In xplor 3.1, It looks go through but the sigma_bonds comes from the last
assigned selection and this script also did not work .
Is there some tricks that I should try?
I would appreciate any suggestions. With many thanks in advance
Satoshi Fujii