Hi Joel,
There will only be 2 frames in the first and last ones.
HTH,
Sjors

> Hi Sjors,
> I supplied a mask and polishing completed without error. I was then able
> to re-refine the polished particles. It makes sense why a mask is needed
> for the B-factor weighting.
>
> I have a followup question: I noticed that using a B-factor running
> average of 3 gives reconstructions corresponding to each frame (38 total).
> However, my understanding is that reconstructions are done for the center
> of each running average, so how are reconstructions made for the 1st and
> 38th frame, which do not fall in the center of a window?
>
> Thanks for your help,
> Joel
>
> On 7/28/15, 4:37 AM, "Sjors Scheres" <[log in to unmask]> wrote:
>
>>Hi Joel,
>>Sorry: it was another thing. Just this morning ran into a similar issue
>>with someone here at LMB. You didn't provide a mask for the B-factor
>>weighting. This is compulsory, but no adequate error was raised in 1.3.
>>I will repair this in 1.4.
>>Could you try again providing a mask?
>>HTH,
>>Sjors
>>
>>On 07/28/2015 02:20 AM, Meyerson, Joel (NIH/NCI) [F] wrote:
>>> Hi Sjors,
>>> As I understand it, particle polishing only sees the _data.star file
>>>that's produced by movie refinement. And, this _data.star file does not
>>>contain any paths to other star files (although it does point to mrcs
>>>files and a group name).
>>>
>>> I ask because in your last e-mail you mentioned the star files from
>>>averaged particles and the movie-frames. Does particle polishing see
>>>these star files, or perhaps other star files that may be causing the
>>>problem?
>>>
>>> Thanks,
>>> Joel
>>> ________________________________________
>>> From: Sjors Scheres [[log in to unmask]]
>>> Sent: Sunday, July 12, 2015 4:03 PM
>>> To: Meyerson, Joel (NIH/NCI) [F]
>>> Cc: [log in to unmask]
>>> Subject: Re: [ccpem] Particle polishing failure in Relion 1.3
>>>
>>> Hi Joel,
>>> Something must be wrong with the input star files. Either the star file
>>> with the averaged particles or (more likely) the movie-frames.
>>> HTH,
>>> Sjors
>>>> Iım running particle polishing in Relion 1.3 and get the following
>>>>output
>>>> (see below). The job fails and does not produce a ³shiny.star² file.
>>>>The
>>>> process is on ~70,000 particles, box size 300, with 38 frames. Nodes
>>>>have
>>>> 32 cores and 128GB memory. For testing I ran on 15 nodes, with 15
>>>> total
>>>> MPI procs and 32 threads per node.
>>>>
>>>> What might the failure be attributable to? Perhaps a memory issue? Any
>>>> thoughts would be welcome.
>>>>
>>>> =================
>>>>   + Reading the input STAR file ...
>>>>   + Grouping all particles from the same micrographs ...
>>>> Cannot read file  It does not exist
>>>> File: ./src/image.h line: 1040
>>>> Done!
>>>>
>>>
>>> --
>>> 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
>
>


-- 
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