Hi Sean,

These values are only calculated FYI, they are not used for anything
else later on.

So, provided the motion corrected micrographs and the output STAR files
are there, you can just proceed.

HTH,

Sjors



On 09/18/2018 01:14 PM, Sean Connell wrote:
> This morning I had a motion correction job fail while generating the
> logfile.pdf with a segmentation error.  I think it failed creating
> the corrected_micrographs_hist_rlnAccumMotionEarly.eps file as it is
> blank when viewed with gs while the other 3 eps files are fine.  The
> reason I think it failed is related to the fact that in
> the corrected_micrographs.star file the _rlnAccumMotionEarly column
> has a value of 0.000000 for all entries (= problem making histogram
> ??).  I am guessing this value is 0 because the movies are 19 frames
> with a dose of 2.43 e/A/frame, so when calculating which frames to use
> for the Early Motion it cuts off after the first frame as
> the —dose_motionstats_cutoff  sets by default the dose to distinguish
> early/late global accumulated motion at 4 which in my case is reached
> in the second frame.
>
> So basically my question is:  Is the rlnAccumMotionEarly motion data
> used any where else later in the pipeline such that I should rerun
> motion correction but increase the —dose_motionstats_cutoff so I can
> get reasonable numbers for _rlnAccumMotionEarly?  Is there an optimal
> number of frames to be using ?
>
> Many thanks for your help and also Relion in general,
>
> Sean
>
> PS continuing the motion correction job with —dose_motionstats_cutoff
> 10 completes with no issue.
>
>
>
>
>  
>
>  
>
> Center of Excellence Severo Ochoa *
>
> Center of Excellence Severo Ochoa (2017-2021)
>
> This e-mail comes from CIC bioGUNE. The e-mail and any files
> transmitted with it are confidential and intended solely for the use
> of the individual or entity to which they are addressed. Any
> unauthorised dissemination or copying of this e-mail or its
> attachments, and any use or disclosure of any information contained in
> them, is strictly prohibited and may be illegal. If you have received
> this e-mail in error, please notify or telephone +34 944 06 13 00 us
> and delete it from your system.
>
> Please consider the environment before printing this email
>
> *
> ------------------------------------------------------------------------
>
> 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