[ccp4bb]: Temperature factor for SE in SE-MET & script

["J. J. Müller" <jjm@mdc-berlin.de>]

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Dear all-
we solved the structure of a Se-Met derivative (refmac 4.1.1; reso. 1.96

A, Rfree=18, Rwork=15%) with 6 Se inside, and we found always the
temperature factor of Se being larger than for CG and CE in MET. The
differences are not tremendous but significant (e. g. 27 A**2 for SE, 20

for CG and CE).
Is there no restrain by default, or do we make a mistake in refinement?
The Van der Waals radius has
been choosen to
VDWR SE 7 3.8.
All suggestions are appreciated.
Cheers.
Jürgen J. Müller

=============================
#!/bin/csh -f
#  Set parameters
#
set SCRATCH =  /usr/dadisk04/scratch
#
set name = 6-516wasser

set log_refmac = $name.log
set log_protin = $name.log
set logfile = {$name}_map.log
set inmtz = ../6-516wasser3/6-516wasser3_9.mtz
echo " " >$log_protin
echo " " >$log_refmac
start:
set last = 0
set cycles = 10
set lastmap = 9
set count = 0
while ($count != $cycles)
echo
'*******************************************************************'
echo  $count
echo
'*******************************************************************'
@ curr = $last + 1
#   Run protin  to set up geometric restraints
#   PROTCOUNTS contains the number of distances, chiral centres,etc..
#   PROTOUT    contains atomic coordinates plus all possible restraint
#              pairings.
#############################################################
protin                          \
XYZIN $SCRATCH/${name}${last}.pdb \
PROTOUT $SCRATCH/protout.dat            \
PROTCOUNTS $SCRATCH/counts.dat          \
<< eop>>$log_protin
!CHNNAME  ID=chain iden;CHNTYP=match CHNTYP;ROFFSET=start resid
CHNNAM ID  A  CHNTYP 1
CHNNAM ID  Y  CHNTYP 2
CHNNAM ID  Z  CHNTYP 2
CHNNAM ID  X  CHNTYP 2
CHNTYP 1  NTER 6 ALA 3  CTER 516 ILE 2
CHNTYP 2 WAT
PEPP 5
SYMM 146
VDWRadii 2 Se 7 3.8 Mn 8 2.7
VDWCUT 5
END
eop
if ($status) exit
#############################################################
#
# Refmac step. Refine
#   PROTSCR    - an abbreviated version of PROTOUT
#                it contains atomic coordinates plus all restraint
#                pairings for atoms which actually are present.
#
refmac:
refmac \
HKLIN   $inmtz \
HKLOUT   $SCRATCH/${name}${last}.mtz \
        PROTOUT $SCRATCH/protout.dat \
        PROTCOUNTS $SCRATCH/counts.dat \
        PROTSCR $SCRATCH/counts.scr \
XYZIN   $SCRATCH/${name}${last}.pdb \
XYZOUT  $SCRATCH/${name}${curr}.pdb \
<< eor>>$log_refmac
LABIN FP=FP SIGFP=SIGFP  FREE=FreeR_flag
LABO FC=FC PHIC=PHIC FWT=2FOFCWT PHWT=PH2FOFCWT -
                     DELFWT=FOFCWT  PHDELWT=PHFOFCWT
REFI TYPE RESTrained RESOLUTION  20 1.94
REFI RESI MLKF
REFI BREF ISOTropic
REFI METH CGMAT
WEIGHT EXPE MATRIX 0.4
!Scaling parameters
SCAL TYPE BULK LSSC ANISO
NCYC 5
MONI MANY
BINS 20
end
eor
#
if ($status) exit
# make maps.
#
#  Sigmaa style 2mfo-dfc map with restored data
#
fft: