Known issue: Difference between revisions

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=== Higher point-group symmetries don't work when compiling in single-precision ===
=== Higher point-group symmetries don't work when compiling in single-precision ===


This bug was reported by David Hasselbach. Change line 94 of <code>src/macros.h</code> from  
This bug was reported by David Hasselbach. Any 3D refinement/classification with symmetries beyond the cyclic ones just won't start. Change line 94 of <code>src/macros.h</code> from  


  #define XMIPP_EQUAL_ACCURACY 1e-6
  #define XMIPP_EQUAL_ACCURACY 1e-6

Revision as of 11:15, 10 September 2015

Release 1.4

Movie-refinement does not work with particles_movie.star file made in release-1.3

In the header of the particles_movie.star rename rlnParticleName to rlnOriginalParticleName.

Higher point-group symmetries don't work when compiling in single-precision

This bug was reported by David Hasselbach. Any 3D refinement/classification with symmetries beyond the cyclic ones just won't start. Change line 94 of src/macros.h from

#define XMIPP_EQUAL_ACCURACY 1e-6

into:

#ifdef FLOAT_PRECISION
#define XMIPP_EQUAL_ACCURACY 1e-4
#else
#define XMIPP_EQUAL_ACCURACY 1e-6
#endif

Release 1.3

Autopicking program crashes with a buffer overflow error

This bug was reported by Gokhan Tolun. When writing out FOM-maps in the autopicking program, it crashes with an error saying "buffer overflow detected". Jean-Christophe Taveau found the bug and suggested the following fix. Line 99 in src/rwSPIDER.h:

char ctim[8]; // 214-215 creation time

Should be:

char ctim[9]; // 214-215 creation time

Movie-extraction with first frame not being number 1

This bug was reported by Wei lu. When extracting movie particles and NOT starting from the first movie frame, then the last few frames are not extracted. Fix lines 512-513 in src/preprocessing.cpp:

if (iiframe >= n_frames)
    return;

Should be:

if (iiframe >= movie_first_frame + n_frames)
    break;

Release 1.2

NaN intensity scales in data_model_groups after 1 or 2 iterations

In some cases refinement runs crash after 1 or 2 iterations and all intensity scales in the data_model_groups table become NaN. The actual cause lies elsewhere, but a good solution is changing line 1890 in src/ml_optimiser.cpp:

mymodel.scale_correction[igroup] = 0.;

should be:

mymodel.scale_correction[igroup] = 1.;

This bug does not affect runs that do not crash.


Release 1.1

Reconstruction sometimes gives strong stripy artifacts

This is a nasty bug in the reconstruction algorithm, which mostly seems to affect reconstructions from many particles, and only the 3D auto-refine option. The effects on the reconstruction can be disastrous: your molecule may disappear completely and you may end up with a stripy pattern instead. Note that if this happens in only one of the two half-reconstructions, it may go by unnoticed (if you don't inspect both half-reconstruction at each iteration) and may just appear as a sudden drop in resolution during the 3D auto-refine optimization. Somehow, this bug is system-dependent and sometimes hard to reproduce.

However, it seems the bug can be circumvented by changing line 658 in src/backprojector.cpp from:

double myfsc = XMIPP_MAX(0., DIRECT_A1D_ELEM(fsc, i));

to:

double myfsc = XMIPP_MAX(0.001, DIRECT_A1D_ELEM(fsc, i));

Then recompile relion using:

make -j 4 && make install

Thanks to Dieter Blaas (Max F. Perutz Laboratories, Vienna) for reporting this bug. It will be fixed in the next release.