1. Did you use relion preprocessing to normalise the images? If so, also
make sure there are no black or otherwise strange particles
2. Try running em2em to convert your MRC files in a format that is read
adequately.
HTH,S
> Hi,
>
>
> I have two problems.
>
> First, I was running 3D auto-refine and got many warning like this:
> "WARNING: norm_correction= ### for particle ## in group1; Are your groups
> large enough?"
>  Although auto-refine was still running, the resulting structures were
> mess.
>
> Second, the other project. I was running preprocessing, and got this ERROR
> :
> "ERROR: cannot find line with Final values in Micrographs/###_ctffind3.log
> File: src/preprocessing.cpp line: 329'
>
> The infos in the .log file is following:
> "
>  CTF DETERMINATION, V3.5 (9-Mar-2013)
>  Distributed under the GNU General Public License (GPL)
>
>  Input image file name
> Micrographs/herbstman00997.mrc
>
>
>
>  Output diagnostic file name
> Micrographs/herbstman00997.ctf
>
>
>
>  CS[mm], HT[kV], AmpCnst, XMAG, DStep[um]
>   2.0    120.0    0.10  132500.0   15.000
>
>  Positive defocus values for underfocus
>  Box, ResMin[A], ResMax[A], dFMin[A], dFMax[A], FStep[A], dAst[A]
>   ERROR reading CARD 4. Trying old CARD 4...
>  512      150.0        5.0    5000.0   50000.0  500.0
>
>   Setting DAST = 100.0
>
>  Opening MRC/CCP4 file for READ...
>  File      : Micrographs/herbstman00997.mrc
>   WARNING: NO MACHINE STAMP
>  NX, NY, NZ:   4096  4096     1
>  MODE      : int*2
>  Min, max  :     1405.000        5696.000
>  Mean, RMS :     2193.320        0.000000
>  TITLE    1:  300000  120000   75000  1    0.1176  0.0014517
>
>
>  READING IMAGE...
>  NX, NY=       4096      4096
> Cannot use file - no file name. Open file first.
> "
> Then I gave the permission to these mrc file, but it's the same error.
>
> Using 'header' program got the header file of one micrograph, like this:
> "
> RO image file on unit:  1 Micrographs/herbstman00994.mrc
>
>  Image Size (X,Y,Sections)...............   4096 4096    1
>  Data Organization (NZ,NW,NT)............      1    1    1
>  Image Sequence..........................  Z -> T -> W
>  Multi-Resolution Settings...............    1  1
>  Data Type...............................  2 Byte Integer
>  Start Pixel / Grid Spacing (X,Y,Z)......     0   0   0  40964096  1
>  Pixel Size..............................    1.000      1.000      1.000
>  Cell Angles.............................    90.00  90.00  90.00
>  Origin (X,Y,Z)..........................    0.000      0.000      0.000
>  Minimum Intensity.......................    1502.00
>  Maximum Intensity.......................    3165.00
>  Mean    Intensity.......................    2201.65
>  Rotation Angles (X,Y,Z).................     0.00   0.00   0.00
>  Crystallography Space Group Number......       0
>  Extended Header Size (Bytes)............  131072
>  Image Type..............................       0
>  Lens ID Number..........................       0
>  Number of Wavelengths...................    1
>  Wavelengths (nm)........................     0
>  Titles ( 1).............................
>   300000  120000   75000  1    0.1176  0.001363
>  section,tilt=      0     0.000
> "
>
> What could I do?
>
> Thanks for your help.
> Yan
>


-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres