Error reading CARD 6
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Dear all,
I would like to use frealign_v08.09 and after I prepared the image stack file containing the particles and the EM map, when I send the script I get the following error:
#PGFIO-F-217/list-directed read/internal file/attempt to read past end of file. In source file card6.f, at line number 27 0.000u 0.001s 0:00.01 0.0% 0+0k 8+8io 0pf+0w cp Frhnegtilt_params_1.par /home/luciccar/Frh-tilt-pairs/ccd/test2/. cp: cannot stat `Frhnegtilt_params_1.par': No such file or directory
It is worth to tell that I do not have the matching projection file needed in card9 but if I am right, in the way I have choosen (FMATCH=T) it will be generated as output by Frealign.
And I do not have any .par and .shft file, but they should be generated as output too.
Are either the .par or the .shft files needed as input?
Thanks in advance,
Luciano
Hi Luciano, Frealign does not
Hi Luciano,
Frealign does not require a .shft file as input, but does require a .par file.
This can be a dummy file containing the defocus parameters for your particles (as generated by imagic2frealign) or can be generated using frealign in mode -3 or -4.
Axel
Dear Axel, thanks for the
In reply to Hi Luciano, Frealign does not by Axel
Dear Axel,
thanks for the information.
In my script I have chosen -4 and tryed -3 too, but I always get the same error. You may have a look at the script here:
M,-4,F,F,F,F,0,F,F,T,0,F,4 !CFORM,IFLAG,FMAG,FDEF,FASTIG,FPART,IEWALD,FBEAUT,FCREF,FMATCH,IFSC,FSTAT,IBLOW 100.,0.,3.57,0.05,0.,100.,35.,200.,500,10 !RO,RI,PSIZE,WGH,XSTD,PBC,BOFF,DANG,ITMAX,IPMAX 1 1 1 1 1 !MASK 1,253 !IFIRST,ILAST D12 !ASYM symmetry card (I=icosahedral) 1., 14.0, 25., 90., 2., 200., 0., 0. !RELMAG,DSTEP,TARGET,THRESH,CS,AKV,TX,TY 10.0, 100.0, 35.0, 150.0, 0. !RREC,RMAX1,RMAX2,DFSIG,RBFACT Frhnegtilt_all_2x2.pad Frhnegtilt_matching_images_${run}.pic 150,79600.,0001,35198,34476,41.,1 !NIN,ABSMAGPIN,IFILMIN,DFMID1IN,DFMID2IN,ANGASTIN,MORE 103,79600.,0002,30783,30841,5.,1 !NIN,ABSMAGPIN,IFILMIN,DFMID1IN,DFMID2IN,ANGASTIN,MORE Frhnegtilt_params_${run}.par Frhnegtilt_shifts.shft 0., 0., 0., 0., 0., 0., 0., 0. ! terminator with RELMAG=0.0 Frh_3dneg_pad_3x3x3_120_${run}.map Frhnegtilt_weights Frhnegtilt_qfactor Frhnegtilt_amplitudes Frhnegtilt_phasediffs Frhnegtilt_pointspread eot # cp Frhnegtilt_params_${run}.par ~/Frh-tilt-pairs/ccd/test2/. #Hi Luciano,The only error I
In reply to Dear Axel, thanks for the by luciano
Hi Luciano,
The only error I can spot is that the final 1 in the line
should be replaced with a 0 to indicate the end of the input.
Axel
Axel,thank you very much,
In reply to Hi Luciano,The only error I by Axel
Axel,
thank you very much, but I still get this error:
Hi luciano, I am a bit
In reply to Axel,thank you very much, by luciano
Hi luciano,
I am a bit confused by the error, as your card 6 looks fine to me.
Could you run the scripts interactively and tell me what the output from frealign looks like?
Thanks,
Axel
I type the parameteres one
In reply to Hi luciano, I am a bit by Axel
I type the parameteres one after the other and things work until it asks for "Matching Projections Image Stack".
You may see the details here:
CFORM,IFLAG,FMAG,FDEF,FASTIG,FPART,IEWALD, FBEAUT,FCREF,FMATCH,IFSC,FSTAT,IBLOW? M,-4,F,F,F,F,0,F,F,T,0,F,4 M -4 F F F F 0 F F T 0 F 4 RO,RI,PSIZE,WGH,XSTD,PBC,BOFF,DANG,ITMAX,IPMAX? 100.,0.,3.57,0.07,0.,100.,35.,200.,500,10 100.0 0.0 3.57 0.070 0.000 100.0 35.0 200.0 500 10 MASK for parameter refinement (e.g. 1 1 1 1 1) ? 1 1 1 1 1 1 1 1 1 1 FIRST, LAST PARTICLES ? 1,253 1 253 SYMMETRY CARD ? D12 D12 Entering GETSYMMAT with ASYM,NASYM D 12 Symmetry point group D12 redundancy 24 MAGNIFICATION, STEPSIZE, TARGET & THRESH PHASE RESIDUAL LIMIT, CS, KV, BEAM TILT X,Y ? 1., 14.0, 25., 90., 2., 200., 0., 0. 1.0 14.0 25.0 90.0 2.0 200.0 0.0 0.0 NSET= 1, RELMAG= 1.000, DSTEP= 14.00 RESOLUTION RECONST., REFINE LOW/HIGH, DFSTD, RBFACT ? 10.0, 100.0, 35.0, 150.0, 0. 10.0 100.0 35.0 150.0 0.0 PARTICLE IMAGE STACK ? Frhnegtilt_all_2x2.pad Frhnegtilt_all_2x2.pad Opening MRC/CCP4 file for READ... File : Frhnegtilt_all_2x2.pad NX, NY, NZ: 50 50 253 MODE : real Min, max : -661.7437 1446.587 Mean, RMS : -43.85558 0.000000 TITLE 1: JOINSTK: Joined MAPFORMAT Files hole1_tilt+5picture1 Feb 10 16:38:20 20 TITLE 2: hole2_tilt+5picture1 Feb 10 16:38:20 20 TITLE 3: LABEL Mode 4: Pixel averaging factor for X,Y,Z = 2 2 1 TITLE 4: PADBOX: file round edge padded by 0 0 0 0 0 0 Feb 15 17:00:54 2012 MATCHING PROJECTIONS IMAGE STACK ? Frhnegtilt_matching_images_1.pic Frhnegtilt_matching_images_1.pic Padding reference volume, IPAD = 4 Interpolation radius for reference IRADA = 1it stays like this and doesn't ask for the next card
Are you sure that there is no
In reply to I type the parameteres one by luciano
Are you sure that there is no further output after you enter the matching projection stack. It might simply take a while until Frealign has finished calculating the big 3D Fourier transform.
Regarding your earlier error in Card 6, please make sure that you keep the formatting of the numbers as they appear in the examples that come with the Frealign distribution. This means that floating point numbers have to have a decimal point and integers do not. I cannot see a mistake in your input here but maybe some of your runs were affected by unintentional format changes.
When I use Frealign
In reply to Are you sure that there is no by niko
When I use Frealign interactively I always get this and waited one day without finding anything changed and also could not see any process running.
But every time I send the script I get the same error in card 6.
I will wait more time that Frealign calculates the 3D Fourier transform and will check even more carefully that the formatting of numbers stays as the template script.
Thank you very much,
Luciano
If you'd like, please run the
In reply to When I use Frealign by luciano
If you'd like, please run the search example script that comes with Frealign (frealign.com, in subdirectory examples/search) and then follow this by this script:
#!/bin/csh -x # set cdir = `pwd` set SCRATCH = ../scratch cd $SCRATCH # # This job requires 2 seconds per particle (AMD Opteron) to determine orientations # from scratch, so 200 particles take about 7 minutes. # \rm -f pdh_shifts_3.shft \rm -f pdh_3.par \rm -f pdh_weights_3 cp -p ${cdir}/pdh_2.mrc pdh_3.mrc # time ../../bin/frealign_v8.exefrealign.com used mode = -3 whereas the script here uses mode = 3. They should both be running very fast and complete in one to two minutes.
The 2 scripts work perfectly
In reply to If you'd like, please run the by niko
The 2 scripts work perfectly fine
If these scripts work you
In reply to The 2 scripts work perfectly by luciano
If these scripts work you should model your own scripts after them. If you observe all the formatting they should run without giving you errors.