Dear CCP4bb-ers,
I have come across a problem with Refmac when I do a few cycles of rigid
body refinement. Somewhere in the process I lose all the hydrogen atoms
from the input pdb file even though I'm using the 'hout YES' option.
Refmac version (from log file):
CCP4 6.0: Refmac_5.2.0019 version 5.2.0019 : 06/09/05
Script:
refmac5 \
XYZIN pdb1abc.ent \
XYZOUT 1abc_refmacrb.pdb \
HKLIN 1abc.mtz \
HKLOUT 1abc_refmacrb.mtz \
<<eof >1abc_rb.log
make check NONE
make -
hydrogen YES -
hout YES -
peptide NO -
cispeptide YES -
ssbridge YES -
symmetry YES -
sugar NO -
connectivity NO -
link NO
refi -
type RIGID -
resi MLKF -
meth CGMAT
rigid ncycle 10
scal -
type SIMP -
LSSC -
ANISO -
EXPE
solvent YES -
VDWProb 1.4 -
IONProb 0.8 -
RSHRink 0.8
weight -
MATRIX 0.1
monitor MEDIUM -
torsion 10.0 -
distance 10.0 -
angle 10.0 -
plane 10.0 -
chiral 10.0 -
bfactor 10.0 -
bsphere 10.0 -
rbond 10.0 -
ncsr 10.0
labin FP=FP SIGFP=SIGFP -
FREE=FREE
labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT
FOM=FOM
PNAME unknown
DNAME unknown220206
RSIZE 80
END
eof
if($status) then
echo "Problem with refmac. Cannot continue."
exit(1)
endif
Is there anything wrong with my script or should this be considered a
bug/feature of refmac?
Thanks for the help,
Robbie Joosten
Center for Molecular and Biomolecular Informatics
Nijmegen, The Netherlands
