Agreed! In most cases the warnings are rather harmless, and one can always
group particles in the Subset Selection jobtype.
HTH,
Sjors
> Hi Dr Heumann
>
> You can remove the micrographs directly from the GUI without needing sed.
> Those warnings harmless AFAIK . Grouping by defocus is possibly more
> helpful than per micrograph
>
> Sincerely.
> Joshua
>
>
>
> On Fri, 12 Oct 2018, 21:11 John Heumann, <[log in to unmask]>
> wrote:
>
>> We have a dataset in which most micrographs contain 200 - 300 particles,
>> but a minority contain few or even no particles after 3D classification
>> and
>> selection. Rather than regrouping all the data, it's been my practice to
>> gather the list of offending micrographs during an initial run of
>> re-extraction with refined coordinates, then to delete the corresponding
>> entries from the selected particles.star file with sed, and finally to
>> run
>> a fresh extraction with the reduced set of refined coordinates. Is this
>> reasonable? When I do this, the number of extracted particles is reduced
>> as
>> I'd expect, but for some reason there are still warnings during
>> extraction
>> about micrographs with too few particles. Are these ignorable?
>>
>> On a related note, I see from the Subsets tab in Subset Selection that
>> there's new (or possibly in progress) work to facilitate screen based on
>> various criteria. Would it be possible to include min / max number of
>> particles per micrograph to such screens in the future?
>>
>> Thanks!
>> -jh-
>>
>> ########################################################################
>>
>> To unsubscribe from the CCPEM list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>>
>
> ########################################################################
>
> To unsubscribe from the CCPEM list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>
--
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
########################################################################
To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
|