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Re: [ccp4bb]: scaling problem
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Dear Jurgen,
Try to use newer version of refmac (either from york's ftp
ftp://ftp.ysbl.york.ac.uk/pub/garib/) or from the ccp4 4.2
(http://www.ccp4.ac.uk)
This problem has been dealt with (I think)
regards
Garib
On Friday 14 Jun 2002 7:29 am, J. J. Müller wrote:
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> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> Dear All,
> coming from a SAD-data set, SOLVE/RESOLVE to refmac
> a scaling problem came up with CCP4 v4.01.
> Neither isotropic nor anisotropic scaling works,
> what is going wrong?
> Thanks,
> Jürgen J. Müller
>
> *****************SCALING***************
> Scale and B factors calculated by log scaling = 0.9897
> -13.24
> log scaling is minimization of
> sum(ln(FO)-ln(FC)-log(scale)+sin^2(th/lm)*B)
> Number of reflection used for scaling= 39829
> ***************************************
>
> Maximum number of refinement cycles 10
> Initial values of K-s and B-s
> 1 0.990 -13.241
> 2 -0.750 200.000
> cycles number 0
> Value of functional = 0.118956E+11
> Current values of K-s and B-s
> 1 1.318 -2.553
> 2 -0.607 70.000
> cycles number 1
> Value of functional = 0.115204E+11
> Current values of K-s and B-s
> 1 1.680 1.859
> 2 -0.940 70.000
> cycles number 2
> Value of functional = 0.112335E+11
> Current values of K-s and B-s
> 1 1.681 1.284
> 2 -0.871 70.000
> cycles number 3
> Value of functional = 0.111168E+11
> Current values of K-s and B-s
> 1 1.681 1.286
> 2 -0.871 70.000
> cycles number 4
> ===> Warning: Minimisation does not work <====================
> ===> Warning: Abnormal termination of parameter estimation<==========
> Maximum number of refinement cycles 10
> Initial values of K-s and B-s
> 1 1.681 1.284 0.000 0.000 1.284 0.000
> 1.284
> 2 -0.871 70.000
> cycles number 0
> Value of functional = 0.111168E+11
> Current values of K-s and B-s
> 1 1.682 1.456 0.239 0.000 1.491 0.000
> 0.609
> 2 -0.872 70.000
> cycles number 1
> Value of functional = 0.111142E+11
> Current values of K-s and B-s
> 1 1.690 1.553 0.349 0.000 1.578 0.000
> 0.710
> 2 -0.875 70.000
> cycles number 2
> ===> Warning: Minimisation does not work
> ===> Warning: Abnormal termination of parameter estimation
> Overall isotropic B = 1.3023
>
>
> Refmac-script
> #############################################################
> # CCP4 v4.01
> # 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 -
> HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM
> LABO FC=FC PHIC=PHIC FWT=2FOFCWT PHWT=PH2FOFCWT -
> DELFWT=FOFCWT PHDELWT=PHFOFCWT
> REFI TYPE RESTrained RESOLUTION 20 1.94
> REFI PHASed SCBL 0.9 BBLUr 20.0 ! " Blur" (ie Scale down)
> FOMs
> REFI PHASE ! use phased Fo Fc
> differences for sigmaA estimation
> REFI RESI MLKF
> REFI BREF ISOTropic
> REFI METH CGMAT
> WEIGHT EXPE MATRIX 0.5
> !Scaling parameters
> SCAL TYPE BULK LSSC ANISO
> NCYC 5
> MONI MANY
> BINS 20
> end
> eor
> #
> if ($status) exit
> # make maps.
> #
--
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 432565