Error reading CARD 6

Submitted by luciano on
Forums
Frealign

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

Axel Tue, 2012-02-14 11:28

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

luciano Tue, 2012-02-14 11:38

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/.
#

Axel Tue, 2012-02-14 12:10

Hi Luciano,

The only error I can spot is that the final 1 in the line

103,79600.,0002,30783,30841,5.,1 	!NIN,ABSMAGPIN,IFILMIN,DFMID1IN,DFMID2IN,ANGASTIN,MORE

should be replaced with a 0 to indicate the end of the input.

Axel

luciano Wed, 2012-02-15 04:34

Axel,

thank you very much, but I still get this 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 0.002s 0:00.00 0.0%      0+0k 8+8io 0pf+0w

Axel Wed, 2012-02-15 10:26

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

luciano Wed, 2012-02-15 11:13

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 =            1

it stays like this and doesn't ask for the next card

niko Wed, 2012-02-15 11:30

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.

luciano Wed, 2012-02-15 11:45

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

niko Wed, 2012-02-15 12:16

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.exe  eot
M,3,F,F,F,F,0,T,T,T,0,F,4                       !CFORM,IFLAG,FMAG,FDEF,FASTIG,FPART,IEWALD,FBEAUT,FCREF,FMATCH,IFSC,FSTAT,IBLOW
146.,0.,3.11,0.07,0.,100.,35.,50.,10,10         !RO,RI,PSIZE,WGH,XSTD,PBC,BOFF,DANG,ITMAX,IPMAX
1,1,1,1,1                                       !MASK
1,200                                           !IFIRST,ILAST 
I                                               !ASYM symmetry card (I=icosahedral)
1., 14.0, 25., 90., 2., 120., 0., 0.            !RELMAG,DSTEP,TARGET,THRESH,CS,AKV,TX,TY
10.0, 100.0, 35.0, 150.0, 0.                    !RREC,RMAX1,RMAX2,DFSIG,RBFACT
${cdir}/../pdh_stack.mrc
pdh_match.mrc
${cdir}/pdh_2.par
pdh_3.par
pdh_3.shft
0., 0., 0., 0., 0., 0., 0., 0.                  !terminator with RELMAG=0.0
pdh_3.mrc
pdh_weights_3
pdh_map1_3
pdh_map2_3
pdh_phasediffs_3
pdh_pointspread_3
eot
#
cp pdh_3.par ${cdir}
cp pdh_3.mrc ${cdir}

frealign.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.