Hi Ben,
Great! Yes, it is important that all the (relative!) paths are valid of
course.
Regarding your question: the map should be UNSHARPENED. I would use the
run1_class001.mrc that comes out of the auto-refine procedure at the
end. That one has the 2 halves combined, but has no sharpening or
filtering (other than the Bayesian regularization).
HTH,
Sjors
On 09/07/2015 11:12 AM, Benoît Zuber wrote:
> 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
>>
--
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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