Hi Liz,
You can only do movie processing after a particle has been included in the
auto-refine.
Also, be always careful when combining STAR files yourself: check the
order and the number of labels and change if necessary. You could indeed
insert dummy values if you don't have any.
Then, relion-1.3 is a bit fuzzy about the rlnParticleName. It is used in
the movie expansion. It is just a number from 1 to N, but if you combine 2
different STAR files, you have to make sure each number occurs only once
(you can renumber yourself, the actual values don't matter). This will no
longer be necessary in relion-1.4 (which will still take another half-year
or so).
HTH,
S

> Hi All
>
> I am at the step of refinement with movie particles and particle
> polishing. After doing movie expansion/refinement step, I noticed that the
> output star file contains less particles than the input star file -
> approximately 1% of my particles. I tracked down that all the missing
> particles come from 18 micrographs. The movie files of these 18
> micrographs exist, and I am able to visualize the movie particles for
> those micrographs, so they were all extracted fine. I finally checked the
> header of these particular particle star files, and then I am able to find
> the problem - the headers are different from the others, so that there are
> 8 data labels in the 'good' files and 5 in the unused ones, moving the
> _rlnParticleName from col 8 to col 5. This ends up being because those 18
> micrographs had some bad sections on them (too much support carbon, for
> example) so I had actually just cleared the autopicked particles and
> manually picked the ones I wanted it, rather than unclicking all the 'bad'
> particles like normal. Yes, yes... I know... greedy, I probably should
> have just thrown those micrographs away...
>
> This long winded explanation leads me to a few questions:
> 1) Is it OK to be missing these particles during the particle polishing
> step?
> 2) If not ok, can I "fix" the particle star files by putting in some value
> into the rlnAnglePsi,_rlnAutopickFigureOfMerit, _rlnClassNumber columns,
> and if so what are good dummy values to put in?
>
> thanks in advance
> Cheers
> Liz
>


-- 
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