Known issue

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Reporting issues

Because many different users may use the program in many different ways, it is difficult to cover all possible cases during testing and evaluation of new features. If you find unexpected errors or results, we urge you to report any and all issues though the issue-tracker at github. If you have suggestions or enhancement suggestions, the issue-tracker is also the correct route.

Known issues

Release 1.4

Seemingly random MPISend-related crashes

On some systems, a nasty bug causes almost random crashes of the parallel version of relion_refine. This bug was reported by Benoit Zuber. Change line 405 in src/ml_optimiser_mpi.cpp from:

length_fn_ctf = exp_fn_img.length() + 1; // +1 to include \0 at the end of the string

into:

length_fn_ctf = exp_fn_ctf.length() + 1; // +1 to include \0 at the end of the string

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.

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