Hi Sjors,
Thank you for your reply. Problem spotted: I was running relion_project
from a subdirectory in my relion project. Then the relative paths to the
particles were not pointing to the particlesŠ
Running it now from relion main directory works.
A general question about the process: do you recommend to use an
unfiltered half map or the filtered and B-factor sharpened map as the
starting point to generate the « yellow.mrc » map?
Best wishes
Ben
Le 06.09.15 22:02, « Sjors Scheres » <[log in to unmask]> a écrit :
>Hi Ben,
>The crash upon completion is not pretty but harmless. When using the
>--subtract_exp option: are your particles and the map the same dimensions?
>Do all particles in the STAR file exist?
>HTH,
>Sjors
>
>
>> Dear Sjors and list
>>
>> I have a segmentation fault occuring with relion_project
>>
>> I use the same options as those given in the latest gamma secretase
>>paper
>> (‹subtract_exp etc.)
>>
>> It is somewhat mysterious: first time I used it it ran until it created
>> the particle star file and then crashed with a segmentation fault. So I
>> could use the star file and the corresponding mrcs particle file to run
>>a
>> reconstruction.
>>
>> Now it crashes just after reading the input star file. No mrcs or star
>> file is created. I get this output (just the last lines are copied
>>here):
>> Done reading STAR file!
>> 000/??? sec ~~(,_,">
>> [oo]Segmentation fault (core dumped)
>>
>> If I now remove ‹subtract_exp, the program runs until it has written the
>> mrcs and star files, and then it crashes with this output:
>> Done reading STAR file!
>> 3/ 3 sec
>> ............................................................~~(,_,">
>> Done writing 266 images in temp.star
>> Segmentation fault (core dumped)
>>
>>
>> I am running relion 1.4 compiled with gcc 4.8.4.
>> Any idea of where the bug could come from?
>>
>>
>> Best wishes
>> Ben
>>
>
>
>--
>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
>
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