Multiple data sets

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I read your 2007 JSB paper (FREALIGN: High-resolution refinement of single particle structures) and learned that the frealign can deal with multiple data sets taken at different microscope with different magnification and merge them together? How do I use this feature?

The frealign input parameter file has a block of parameters (input cards 6 - 12) that can be repeated for several data sets, up to 20 times. Example:

1.0,${dstep},${target},90.0,2.0,${kV1},0.0,0.0        !RELMAG,DSTEP,TARGET,THRESH,CS,AKV,TX,TY
${rrec}, 200.0, ${rref}, ${rbf}                       !RREC,RMAX1,RMAX2,RBFACT
${working_directory}/${raw_images1}.mrc
${data_input}1_reproject.mrc_${1}_${2}
${working_directory}/${data_input}1_${prev}.par
${data_input}1_${start}.par_${1}_${2}
${data_input}1_${start}.shft_${1}_${2}
1.0,${dstep},${target},90.0,2.0,${kV2},0.0,0.0        !RELMAG,DSTEP,TARGET,THRESH,CS,AKV,TX,TY
${rrec}, 200.0, ${rref}, ${rbf}                       !RREC,RMAX1,RMAX2,RBFACT
${working_directory}/${raw_images2}.mrc
${data_input}2_reproject.mrc_${1}_${2}
${working_directory}/${data_input}2_${prev}.par
${data_input}2_${start}.par_${1}_${2}
${data_input}2_${start}.shft_${1}_${2}
1.0,${dstep},${target},90.0,2.0,${kV3},0.0,0.0        !RELMAG,DSTEP,TARGET,THRESH,CS,AKV,TX,TY
${rrec}, 200.0, ${rref}, ${rbf}                       !RREC,RMAX1,RMAX2,RBFACT
${working_directory}/${raw_images3}.mrc
${data_input}3_reproject.mrc_${1}_${2}
${working_directory}/${data_input}3_${prev}.par
${data_input}3_${start}.par_${1}_${2}
${data_input}3_${start}.shft_${1}_${2}
-100., 0., 0., 0., 0., 0., 0., 0.                     !terminator with RELMAG=0.0 or -100.0

In this example, there are three different data sets. For each, different DSTEP, TARGET, THRESH, CS, AKV, TX, TY, RREC, RMAX1, RMAX2 and RBFACT parameters can be provided although, in this example, only the voltage changes.

I tried this feature today, to read in my several spider stacks, by repeating cards 6-12. Every time,
though, I get this error, which says the file is connected to another unit. This did not happen with the
two stacks that were read in prior to this point.
-Thanks,
Celia

As follows: ....

Number of images in set 3 = 798 (on 1 new films), total particle parameters so far = 6408

Min, max phase residual = 0.000 0.000
Using X,Y distribution function:
Average X,Y shifts = -0.033 -0.175
Sigma X,Y shifts = 1.507 1.982

OUTPUT PARAMETER FILE ?
f08_gooddataINSK003.spi.par
PGFIO-F-207/OPEN/unit=33/file is already connected to another unit.
File name = f08_gooddataINSK003.spi.par
In source file cards11and12.f, at line number 42
0.0u 0.0s 0:00.09 66.6% 0+0k 0+16io 0pf+0w

In reply to by bohm

It looks like Frealign is trying to open file f08_gooddataINSK003.spi.par a second time. Is it possible that you entered the file name twice in your input list?

In reply to by niko

Hi Niko - as it turns out, I was specifying the same file for card 9 for a second time. I was also very focused on being sure that I hadn't repeated my card 10s (which were all different), that I overlooked the card 9 error. Fresh eyes in the morning, and all that. Thanks! Now I am on to new errors. Perhaps more on that later, but I think it's more Spider conversion issues.
Thanks,
Celia