Hi Joshua,
If you manually pick 'extra' particles, then you cannot run the sort
program directly after that. You would first need to do a 2D
classification, as the sorting needs a reference for each particle.
Usually, the autopick parameters can be adjusted so that all particles are
picked. Perhaps that gives more false positives, but they can typically be
removed in the 2D classification.
HTH,
Sjors
> Hello everyone
>
> I have a question regarding the general procedure followed after the
> auto-pick process is complete in relion 1.3 . I manually removed all the
> false positives (high contrast non particles ) . After cleaning the
> micrographs I also picked some particles which the program seemed to miss
> ( the program is very impressive it got most of the particles the manually
> picked particles would account for say 3-4% of the particles in the data
> set) . In the star file created it added a -999 group number (for the
> manually picked particles ). it returned a >
>
> "Too large class number for the given number of reference"
>
> lets say as an example I had 2 references initially given to the autopick
> program ( the output of the 2D classification) now I feel that the
> manually picked particles ( the ones with the -999 group number) are going
> into a class of their own and hence the sorting program is getting another
> class which it does not recognize.
>
> After autopick is complete is it recommended to just clean the false
> positives and not add any more manually picked particles that the program
> missed?
>
>
> any suggestions or advice are most welcome
> Sincerely
>
> Joshua Lobo
>
--
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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