Known issue: Difference between revisions

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=== Reconstruction sometimes gives strong stripy artifacts ===
=== 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.  
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. Somehow, this bug is system-dependent and sometimes hard to reproduce.
 
The bug can be circumvented by changing line 658 in <code>src/backprojector.cpp</code>
 
from:


However, the bug can be circumvented by changing line 658 in <code>src/backprojector.cpp</code> from:
double myfsc = XMIPP_MAX(0., DIRECT_A1D_ELEM(fsc, i));
double myfsc = XMIPP_MAX(0., DIRECT_A1D_ELEM(fsc, i));


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



Revision as of 09:52, 9 November 2012

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. Somehow, this bug is system-dependent and sometimes hard to reproduce.

However, 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

This will be fixed in the next release.