Hi,
I recall some 'constraints' on the grid numbers; if I remember well, at least y and z have to be even in P1 (and the same grid had to be used in fft to create the map in the first place...)
Less sure than this first limit (so please correct me if I'm wrong!)...two more restriction limits :
care has to be taken with the slow-medium-fast axis order; I thought for SGs l.t. 19 the order should be Z X Y;
the map should cover a CCP4 'conventional' ASU, so looking at your 'start-stop' end points, not sure that is being respected (perhaps simple 0 255 0 255 0 255 would work).
good luck
On 20/03/2008, Bruno Klaholz <[log in to unmask]> wrote:
>
> Dear Larry,
>
> you may have to coarsen and cut your map into 120,120,120 (full
> sampling may not be needed anyway for MR) or try cutting into
> 240,240,240 (though I haven't tried such big values yet).
> I noticed that you have already converted the axes to XYZ (I guess
> with the uvw option in mapman) which is indeed needed.
>
> By the way, sftools does a nice job for getting the reflection file
> with sigmas included (needed for example for structure refinement)
> and the test label on:
>
> sftools <<EOF
> MAPIN map-uvw.ccp4 map
> MAP2SF
> calc q col sigma = col 1 10 /
>
> select resol > 10
>
> CALC I col test = rfree(0.05)
>
> WRITE data-uvw.fobs col 1 3 2 4
> xpl
> FOBS
> PHASE
>
> write
> data-uvw.mtz
> quit
> EOF
> (last part is to check with mtzdump HKLIN whether the reflections
> have correct values)
>
> Bruno
>
>
>
>
>
> >Hello All,
> >
> >I'm trying to back-FT an EM map to produce Fs and phases to use in
> >molecular replacement, but am having a problem with running SFALL.
> >
> >Here's the issue: When running the back-transform in SFALL (generating
> >structure factors from a map), I get the following error:
> >Incorrect sampling grid factors 255 255 255
> >
> >The map parameters are given below. Does anyone have any idea of how
> >to deal with this?
> >
> >Thanks,
> >
> >Larry
> >
> >
> >
> > Number of columns, rows, sections ............... 256 256 256
> > Map mode ........................................ 2
> > Start and stop points on columns, rows, sections -128 127
> >-128 127 -128 127
> > Grid sampling on x, y, z ........................ 255 255 255
> > Cell dimensions ................................. 459.00000
> >459.00000 459.00000 90.00000 90.00000 90.00000
> > Fast, medium, slow axes ......................... X Y Z
> > Minimum density ................................. -1.24222
> > Maximum density ................................. 2.25668
> > Mean density .................................... 0.06370
> > Rms deviation from mean density ................. 0.00000
> > Space-group ..................................... 1
> > Number of titles ................................ 3
> >
> >
> >--
> >Lawrence Shapiro, Ph.D.
> >Associate Professor
> >Dept. of Biochemistry and Molecular Biophysics
> >Jules and Doris Stein Professor of Research to Prevent Blindness
> >Edward S. Harkness Eye Institute
> >Columbia University
> >701 West 168th Street, 7th Floor
> >New York, NY 10032
> >
> >Tel: (212)342-6029
> >Fax: (212)342-6026
> >e-mail: [log in to unmask]
> > [log in to unmask]
> >http://www.shapirolab.org
> >
> >
>
>
>
>
>
>
>
>
>
> ############################################################################
>
> Dr. Bruno P. Klaholz
> Department of Structural Biology and Genomics
> Institute of Genetics and of Molecular and Cellular Biology
> IGBMC - UMR 7104
> 1, rue Laurent Fries
> BP 10142
> 67404 ILLKIRCH CEDEX
> FRANCE
>
>
> Tel. from abroad: 0033.388.65.57.55
> Tel. inside France: 03.88.65.57.55
>
> Fax from abroad: 0033.388.65.32.76
> Fax inside France: 03.88.65.32.76
> e-mail: [log in to unmask]
> websites:
> http://www.igbmc.fr/
> http://igbmc.fr/recherche/Dep_BSG/Eq_BKlah/index_uk.html
>
--
Alejandro Buschiazzo
Research Scientist
Laboratory of Structural Biology
Institut Pasteur de Montevideo
Uruguay
Phone : +5982 5220910 int.120
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