Check the log file carefully that MOSFLM has "swallowed" each of your
script lines. I don't think "stats on" is a valid command. The
strategy command "stats" (with no qualification) is generally run after
the "go" command:
strategy auto
go
stats
end
What is probably happening is MOSFLM is balking on the "stats on" line
and then exits "strategy". The next line is a "go", which means load
the image in graphics.
There is also a program I call "Wedger Elves" which (among other things)
will take a matrix and an image and give you a strategy using MOSFLM.
It will also run LABELIT to do indexing if you have it installed.
http://bl831.als.lbl.gov/~jamesh/elves/
-James Holton
MAD Scientist
Jan Abendroth wrote:
> Hi all,
> I have been trying to use mosflm in script mode, in a quick-n-dirty
> effort to pipe some information from labelit.index into a simple data
> collection strategy. While doing that, I run into the following issue.
> I have not been able to find a way to read in image information
> without starting the old gui. Is there a command in the current mosflm
> versions to run it in shell mode only? Below the script that I have
> been using.
> Any ideas?
>
> Thanks
> Jan
>
>
> ---
> ipmosflm summary integrate02.sum <<eof
> DIRECTORY ../images
> TEMPLATE image_###.img
> IMAGE 1
> HKLOUT integration02.mtz
> GENFILE integration02.gen
> #detector-take defaults
>
> #UIS_PIXEL 0.102400
> #UIS_SIZE 3072
>
> NUSPOT OFF
> BEAM 155.400500 158.807700
> DISTANCE 299.775600
> TWOTHETA 0.0
>
> WAVE 0.977400
> #beam
> SYNCHROTRON POLARIZATION 0.9
> DIVERGENCE 0.100 0.020
> DISPERSION 0.0001
>
>
> MOSAICITY 0.60
> SYMMETRY p2
> RESOLUTION 3.5
> MATRIX integration02.mat
>
> PROFILE OVERLOAD PARTIALS
> RASTER 19 19 9 4 4
> SEPARATION 1.80 1.80 CLOSE
> REFINEMENT RESID 7.5
> REFINEMENT INCLUDE PARTIALS RESID 10.0 #High s/n
>
>
> scanner adsc
> strategy auto
> stats on
> go
> end
> exit
> eof
>
>
> --
> Jan Abendroth
> Emerald BioStructures
> Seattle / Bainbridge Island WA, USA
> home: Jan.Abendroth_at_gmail.com
> work: JAbendroth_at_embios.com
> http://www.emeraldbiostructures.com
>
>
>
>
>
>
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