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Re: [ccp4bb] Back-Fourier transforming an EM map with SFALL
 

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CCP4bb <-- 2008 <-- March 2008 <-- 20 March 2008
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Subject: Re: Back-Fourier transforming an EM map with SFALL
From: Bruno Klaholz klaholz {- at -} TITUS {- dot -} U-STRASBG {- dot -} FR
Date: 2008-03-20

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 <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: shapiro@convex.hhmi.columbia.edu
> lss8@columbia.edu
>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: klaholz@igbmc.u-strasbg.fr
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