Dear Jürgen:
Exactly! 1SS8, the tls-refined GroEL. I generated a PDB containing the
total anistropic B values by TLS, based on which I want to reproduce the R
factor by REFMAC as they used. Thanks for your advice, following is my
script. Unfortunately, it failed to reproduce the PDB R factor...
Not sure whether the NCSR part is correct or not, 'cause the PDB file
provides 3 NCS groups where 2 of them containing mutliple domains (see PDB
header after the REFMAC script...).
Thanks lot!
Hailiang
*****************
#!/bin/bash
PDB="1SS8"
refmac5 \
HKLIN 1ss8-sf.mtz \
HKLOUT ${PDB}-refmac.mtz \
XYZIN ${PDB}.pdb \
XYZOUT ${PDB}-refmac.pdb << eor
#
# Input/output column assignments
#
LABIN FP=FP SIGFP=SIGFP FREE=FREE
LABO FC=FC PHIC=PHIC FWT=2FOFCWT DELFWT=FOFCWT
#
# Type of refinement
#
REFI TYPE REST
REFI RESI MLKF
REFI BREF ISOT METH CGMAT
#
# NCS restraints
#
NCSRestraints NCHAins 7 CHAIns A B C D E F G NSPANS 2 2 135 1 410 525 1
NCSRestraints NCHAins 7 CHAIns A B C D E F G NSPANS 2 136 190 1 375 409 1
NCSRestraints NCHAins 7 CHAIns A B C D E F G NSPANS 1 191 374 1
#
# Scaling, in particular requesting anisotropic scaling
#
SCAL TYPE BULK
SCAL LSSC ANISOT
#
# Other keywords
#
WEIG AUTO
MONI MEDI
NCYC 10
END
eor
***********************
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 3
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 1 C 2 C 135 1
REMARK 3 1 D 2 D 135 1
REMARK 3 1 E 2 E 135 1
REMARK 3 1 F 2 F 135 1
REMARK 3 1 G 2 G 135 1
REMARK 3 2 A 410 A 525 1
REMARK 3 2 B 410 B 525 1
REMARK 3 2 C 410 C 525 1
REMARK 3 2 D 410 D 525 1
REMARK 3 2 E 410 E 525 1
REMARK 3 2 F 410 F 525 1
REMARK 3 2 G 410 G 525 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 POSITIONAL 1 C (A): 1806 ; 0.098 ; 0.050
REMARK 3 TIGHT POSITIONAL 1 D (A): 1806 ; 0.087 ; 0.050
REMARK 3 TIGHT POSITIONAL 1 E (A): 1806 ; 0.108 ; 0.050
REMARK 3 TIGHT POSITIONAL 1 F (A): 1806 ; 0.091 ; 0.050
REMARK 3 TIGHT POSITIONAL 1 G (A): 1806 ; 0.092 ; 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 TIGHT THERMAL 1 C (A**2): 1806 ; 0.189 ; 0.500
REMARK 3 TIGHT THERMAL 1 D (A**2): 1806 ; 0.190 ; 0.500
REMARK 3 TIGHT THERMAL 1 E (A**2): 1806 ; 0.216 ; 0.500
REMARK 3 TIGHT THERMAL 1 F (A**2): 1806 ; 0.182 ; 0.500
REMARK 3 TIGHT THERMAL 1 G (A**2): 1806 ; 0.193 ; 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 1 C 136 C 190 1
REMARK 3 1 D 136 D 190 1
REMARK 3 1 E 136 E 190 1
REMARK 3 1 F 136 F 190 1
REMARK 3 1 G 136 G 190 1
REMARK 3 2 A 375 A 409 1
REMARK 3 2 B 375 B 409 1
REMARK 3 2 C 375 C 409 1
REMARK 3 2 D 375 D 409 1
REMARK 3 2 E 375 E 409 1
REMARK 3 2 F 375 F 409 1
REMARK 3 2 G 375 G 409 1
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
REMARK 3 TIGHT POSITIONAL 2 A (A): 647 ; 0.072 ; 0.050
REMARK 3 TIGHT POSITIONAL 2 B (A): 647 ; 0.076 ; 0.050
REMARK 3 TIGHT POSITIONAL 2 C (A): 647 ; 0.073 ; 0.050
REMARK 3 TIGHT POSITIONAL 2 D (A): 647 ; 0.070 ; 0.050
REMARK 3 TIGHT POSITIONAL 2 E (A): 647 ; 0.083 ; 0.050
REMARK 3 TIGHT POSITIONAL 2 F (A): 647 ; 0.071 ; 0.050
REMARK 3 TIGHT POSITIONAL 2 G (A): 647 ; 0.076 ; 0.050
REMARK 3 TIGHT THERMAL 2 A (A**2): 647 ; 0.109 ; 0.500
REMARK 3 TIGHT THERMAL 2 B (A**2): 647 ; 0.131 ; 0.500
REMARK 3 TIGHT THERMAL 2 C (A**2): 647 ; 0.105 ; 0.500
REMARK 3 TIGHT THERMAL 2 D (A**2): 647 ; 0.108 ; 0.500
REMARK 3 TIGHT THERMAL 2 E (A**2): 647 ; 0.132 ; 0.500
REMARK 3 TIGHT THERMAL 2 F (A**2): 647 ; 0.102 ; 0.500
REMARK 3 TIGHT THERMAL 2 G (A**2): 647 ; 0.134 ; 0.500
REMARK 3
REMARK 3
REMARK 3 NCS GROUP NUMBER : 3
REMARK 3 CHAIN NAMES : A B C D E F G
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 A 191 A 374 1
REMARK 3 1 B 191 B 374 1
REMARK 3 1 C 191 C 374 1
REMARK 3 1 D 191 D 374 1
REMARK 3 1 E 191 E 374 1
REMARK 3 1 F 191 F 374 1
REMARK 3 1 G 191 G 374 1
REMARK 3 GROUP CHAIN COUNT RMS WEIGHT
REMARK 3 TIGHT POSITIONAL 3 A (A): 1398 ; 0.051 ; 0.050
REMARK 3 TIGHT POSITIONAL 3 B (A): 1398 ; 0.049 ; 0.050
REMARK 3 TIGHT POSITIONAL 3 C (A): 1398 ; 0.053 ; 0.050
REMARK 3 TIGHT POSITIONAL 3 D (A): 1398 ; 0.052 ; 0.050
REMARK 3 TIGHT POSITIONAL 3 E (A): 1398 ; 0.062 ; 0.050
REMARK 3 TIGHT POSITIONAL 3 F (A): 1398 ; 0.043 ; 0.050
REMARK 3 TIGHT POSITIONAL 3 G (A): 1398 ; 0.053 ; 0.050
REMARK 3 TIGHT THERMAL 3 A (A**2): 1398 ; 0.074 ; 0.500
REMARK 3 TIGHT THERMAL 3 B (A**2): 1398 ; 0.062 ; 0.500
REMARK 3 TIGHT THERMAL 3 C (A**2): 1398 ; 0.068 ; 0.500
REMARK 3 TIGHT THERMAL 3 D (A**2): 1398 ; 0.071 ; 0.500
REMARK 3 TIGHT THERMAL 3 E (A**2): 1398 ; 0.084 ; 0.500
REMARK 3 TIGHT THERMAL 3 F (A**2): 1398 ; 0.055 ; 0.500
REMARK 3 TIGHT THERMAL 3 G (A**2): 1398 ; 0.071 ; 0.500
REMARK 3
> 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
>
>
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