Known issue
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 -1)
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.