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
