Take a look at this part of a script, I added your NCS operators in two options.
So you are working on GroEL ?
Good luck,
Jürgen
#!/bin/csh -f
set prevVer = 01
set prevRun = 00
set currVer = 02
set currRun = 04nolig
set currData = my_latest_structure
#
set xyzin = omitted_ligands.pdb
set xyzot = v{$currVer}r{$currRun}_{$currData}.pdb
#
#XDS processed data
set hklin = v02r02_Pf_Cmp24.mtz
set hklot = v{$currVer}r{$currRun}_{$currData}.mtz
#
set log = v{$currVer}r{$currRun}_{$currData}.log
#
refmac5 \
HKLIN $hklin HKLOUT $hklot \
# LIBIN Cmp24.cif \
# TLSIN tls_def.tlsin TLSOUT tls.out \
XYZIN tmp.pdb XYZOUT $xyzot \
<<EOF >> $log
MAKE HYDRogens ALL
MAKE CHECK 0
MAKE CISP N BUILD Y
LABI FP=FP SIGFP=SIGFP FREE=FreeR_flag
REFI TYPE RESTrained RESOlution 25 1.7
#option # 1 over the whole chain
#NCSRestraints NCHAins 7 CHAIns A B C D E F G
#or option #2 two domains per chain
#for definitions of restrain codes
# RTFM
# http://www.ccp4.ac.uk/html/refmac5/keywords/restraints.html#ncsr
NCSRestraints NCHAins 7 CHAIns A B C D E F G NSPANS 2 2 135 1 136 190 1
REFI RESI MLKF
#BFACtor SET_to 90
#REFI TLSC 10
REFI BREF ISOT ! Refine overall B-values
WEIG MATR 0.1
DAMP 0.5 0.5
SCALe TYPE BULK
SCALe LSSCale
SCALe LSSCale ANISotropic
SCAL MLSC
NCYC 10
TEMP 1.0 4.0 6.0 6.0 10.0
MONI MANY DIST 4 TORS 4 ANGL 4 CHIR 4 VDWR 3 NCSR 4 PLAN 4 NCSR 4 BFAC 4
BINS 10
EOF
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
On Sep 9, 2010, at 8:29 PM, Hailiang Zhang wrote:
> Hi there:
>
> The REFMAC manual give me a hard time to define the NCS during refinement.
> Can anybody give a first time user a sample script based on the following
> PDB header (NCS part only is ok, but please include how todefine tight
> restrant only for both positional and B ref, for both NCS groups)? Thanks
> a lot!
>
> Best Regards, Hailiang
>
> REMARK 3 NCS RESTRAINTS STATISTICS
> REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2
> REMARK 3
> REMARK 3 NCS GROUP NUMBER : 1
> REMARK 3 CHAIN NAMES : A B C D E F G
> REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2
> REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
> REMARK 3 1 A 2 A 135 1
> REMARK 3 1 B 2 B 135 1
> REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
> REMARK 3 TIGHT POSITIONAL 1 A (A): 1806 ; 0.092 ; 0.050
> REMARK 3 TIGHT POSITIONAL 1 B (A): 1806 ; 0.131 ; 0.050
> REMARK 3 TIGHT THERMAL 1 A (A**2): 1806 ; 0.192 ; 0.500
> REMARK 3 TIGHT THERMAL 1 B (A**2): 1806 ; 0.228 ; 0.500
>
> REMARK 3
> REMARK 3 NCS GROUP NUMBER : 2
> REMARK 3 CHAIN NAMES : A B C D E F G
> REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2
> REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
> REMARK 3 1 A 136 A 190 1
> REMARK 3 1 B 136 B 190 1
> REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
> REMARK 3 TIGHT POSITIONAL 1 A (A): 1806 ; 0.092 ; 0.050
> REMARK 3 TIGHT POSITIONAL 1 B (A): 1806 ; 0.131 ; 0.050
> REMARK 3 TIGHT THERMAL 1 A (A**2): 1806 ; 0.192 ; 0.500
> REMARK 3 TIGHT THERMAL 1 B (A**2): 1806 ; 0.228 ; 0.500
