Hi Sjors,
Thanks for the clarification!
Cheers
Ben
Le 07.09.15 13:04, « Sjors Scheres » <[log in to unmask]> a écrit :
>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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