[ccp4bb] Hydrogens disappear after refmac refinement

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Protein crystallographer position in Novartis, Basel
From: sandra {- dot -} jacob {- at -} NOVARTIS {- dot -} COM sandra {- dot -} jacob {- at -} NOVARTIS {- dot -} COM
Date: 2007-05-15

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Subject: Crystallization Course: focus on membrane proteins 2007- Final Agenda
From: "Stojanoff, Vivian" stojanof {- at -} BNL {- dot -} GOV
Date: 2007-05-15

Subject: Hydrogens disappear after refmac refinement
From: "R {- dot -} P {- dot -} Joosten" rjoosten {- at -} CMBI {- dot -} RU {- dot -} NL
Date: 2007-05-15

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
<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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Crystallization Course: focus on membrane proteins 2007- Final Agenda
From: "Stojanoff, Vivian" stojanof {- at -} BNL {- dot -} GOV
Date: 2007-05-15