I have not altered the STAR files manually.
I followed not the wiki, but the PDF tutorial. I'll check if there are any
difference between the two that may cause such problems.
Have a nice weekend.
Gökhan

-----Original Message-----
From: Sjors Scheres [mailto:[log in to unmask]] 
Sent: Friday, August 29, 2014 5:09 PM
To: "Gökhan Tolun"
Cc: [log in to unmask]
Subject: Re: [ccpem] Particle polishing problem

Often, these types of problems arise when you've somehow manually adjusted
the STAR files... The recommended way to do movie-processing is detailed on
the RELION Wiki. I would suggest to closely follow that.
HTH, S
> Well, that¹s part of the problem I guess. I only have 10 frames in 
> each original micrograph, and for now I am trying to use the first 5 
> to see what happens. So, although I have only 5 frames in the 
> extracted particles, I don¹t know why it generates a set of 105 
> frames. Any suggestions about what to check to find out?
> Dose per frame is 3 e/A2
> Thanks.
> Gökhan
>
>
> On 8/29/14, 12:30 PM, "Sjors Scheres" <[log in to unmask]> wrote:
>
>>Are you sure you want to do a 105-frame movie refinement? I am not 
>>sure at all whether that will actually work. What's the dose per movie
frame?
>>S
>>
>>On 08/29/2014 03:21 PM, Gökhan Tolun wrote:
>>> Dear all,
>>>
>>> I know it is a long message, but I am trying to provide as much 
>>> detail as I can for better troubleshooting, so here it goes.
>>>
>>> I am stuck at the Particle polishing step. The following are the 
>>> problems I am dealing with:
>>>
>>> The job seems to be running, and under Refine3D folder it creates a 
>>> series of files as follows, (the below frame105 is the last one of 
>>> the series),
>>>
>>> run03_mv01_fr5_ct19_data_shiny01_frame105_guinier.star
>>> run03_mv01_fr5_ct19_data_shiny01_frame105_half1_class001_unfil.mrc
>>> run03_mv01_fr5_ct19_data_shiny01_frame105_half2_class001_unfil.mrc
>>>
>>> But only the first five of them have reconstructions, the rest seem 
>>> to be empty.
>>>
>>> The other generated files are:
>>>
>>> run03_mv01_fr5_ct19_data_shiny01_avgframes_half1_class001_unfil.mrc
>>> run03_mv01_fr5_ct19_data_shiny01_avgframes_half2_class001_unfil.mrc
>>>
>>> run03_mv01_fr5_ct19_data_shiny01_bfactors.star
>>>
>>> run03_mv01_fr5_ct19_data_shiny01_relweights.star
>>>
>>> run03_mv01_fr5_ct19_data_shiny01.star
>>>
>>> However, the bfactors file contains
>>>
>>> data_perframe_bfactors
>>>
>>> loop_
>>> _rlnMovieFrameNumber #1
>>> _rlnBfactorUsedForSharpening #2
>>> _rlnFittedInterceptGuinierPlot #3
>>> 1 8.780326 -0.248246
>>> 2 -11.390702 -0.616245
>>> 3 35.885949 -1.085373
>>> 4 -12.895935 -0.995643
>>> 5 -12.415657 -1.082416
>>> 6 -nan -nan
>>> 7 -nan -nan
>>> 8 -nan -nan
>>> 9 -nan -nan
>>> 10 -nan -nan
>>> 11 -nan -nan
>>> 12 -nan -nan
>>> 13 -nan -nan
>>> 14 -nan -nan
>>> 15 -nan -nan
>>> 16 -nan -nan
>>> 17 -nan -nan
>>> 18 -nan -nan
>>> 19 -nan -nan
>>> 20 -nan -nan
>>> 21 -nan -nan
>>> 22 -nan -nan
>>> 23 -nan -nan
>>> 24 -nan -nan
>>> 25 -nan -nan
>>> 26 -nan -nan
>>> 27 -nan -nan
>>> 28 -nan -nan
>>> 29 -nan -nan
>>> 30 -nan -nan
>>> 31 -nan -nan
>>> 32 -nan -nan
>>> 33 -nan -nan
>>> 34 -nan -nan
>>> 35 -nan -nan
>>> 36 -nan -nan
>>> 37 -nan -nan
>>> 38 -nan -nan
>>> 39 -nan -nan
>>> 40 -nan -nan
>>> 41 -nan -nan
>>> 42 -nan -nan
>>> 43 -nan -nan
>>> 44 -nan -nan
>>> 45 -nan -nan
>>> 46 -nan -nan
>>> 47 -nan -nan
>>> 48 -nan -nan
>>> 49 -nan -nan
>>> 50 -nan -nan
>>> 51 -nan -nan
>>> 52 -nan -nan
>>> 53 -nan -nan
>>> 54 -nan -nan
>>> 55 -nan -nan
>>> 56 -nan -nan
>>> 57 -nan -nan
>>> 58 -nan -nan
>>> 59 -nan -nan
>>> 60 -nan -nan
>>> 61 -nan -nan
>>> 62 -nan -nan
>>> 63 -nan -nan
>>> 64 -nan -nan
>>> 65 -nan -nan
>>> 66 -nan -nan
>>> 67 -nan -nan
>>> 68 -nan -nan
>>> 69 -nan -nan
>>> 70 -nan -nan
>>> 71 -nan -nan
>>> 72 -nan -nan
>>> 73 -nan -nan
>>> 74 -nan -nan
>>> 75 -nan -nan
>>> 76 -nan -nan
>>> 77 -nan -nan
>>> 78 -nan -nan
>>> 79 -nan -nan
>>> 80 -nan -nan
>>> 81 -nan -nan
>>> 82 -nan -nan
>>> 83 -nan -nan
>>> 84 -nan -nan
>>> 85 -nan -nan
>>> 86 -nan -nan
>>> 87 -nan -nan
>>> 88 -nan -nan
>>> 89 -nan -nan
>>> 90 -nan -nan
>>> 91 -nan -nan
>>> 92 -nan -nan
>>> 93 -nan -nan
>>> 94 -nan -nan
>>> 95 -nan -nan
>>> 96 -nan -nan
>>> 97 -nan -nan
>>> 98 -nan -nan
>>> 99 -nan -nan
>>> 100 -nan -nan
>>> 101 -nan -nan
>>> 102 -nan -nan
>>> 103 -nan -nan
>>> 104 -nan -nan
>>> 105 -nan -nan
>>>
>>> Then, under the Particles folder, I have only 8 files named Œshiny¹, 
>>>like
>>>
>>> Jun11_19.29.29_e2_part3_shiny01.mrcs
>>>
>>> So, clearly there¹s something wrong, but I cannot see any apparent 
>>> error messages generated.
>>>
>>> Moreover, when I run the script AnalyseMovement.csh, the processing 
>>> of run03_mv01_fr5_ct19_data.stargoes fine but when I run it with 
>>> run03_mv01_fr5_ct19_data_shiny01.starit gives the error ³Word too 
>>> long.² I suspect this may be due to the relatively long file names I 
>>> have, but I do not how I can find a workaround or fix it.
>>>
>>> Have you seen anything like these during your processing, and/or do 
>>> you have any ideas about how to fix them?
>>>
>>> Thanks and have a nice weekend.
>>>
>>> Gökhan
>>
>>--
>>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