[ccp4bb] mosflm in script mode
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
Re: [ccp4bb] mosflm in script mode
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
Re: [ccp4bb] mosflm in script mode
Hi Jan The IMAGE command turns the old gui on - always has done, as far as I know. With Strategy auto you shouldn't need to give an image number. HTH On 28 May 2010, at 14:35, 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 Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
