Hi Sjors,
The micrographs look fine, though as Relion notices some of them have very few particles, including the image I referred to in my e-mail. However, perhaps the pixel values in the micrographs are causing the problem? The pixel values from such (unbinned) micrographs after alignment with IMOD tilltxcorr tend to be like this:
Minimum density ....................... 0.50493E-01
Maximum density ....................... 3.1997
Mean density .......................... 0.15805
Worth mentioning is that if I use data pre-aligned using UCSF motioncorr (bin2) I can then process the data in Relion without problem. These images tend to have pixel values like this:
Minimum density ....................... 15.428
Maximum density ....................... 159.41
Mean density .......................... 53.271
________________________________________
From: Sjors Scheres [[log in to unmask]]
Sent: Tuesday, October 14, 2014 12:19 PM
To: Meyerson, Joel (NIH/NCI) [F]
Cc: [log in to unmask]
Subject: Re: [ccpem] rlnMicrographScaleCorrection is very high
If you inspect the particles on that micrograph: do you see anything
strange?
S
On 10/14/2014 04:57 PM, Meyerson, Joel (NIH/NCI) [F] wrote:
> Hi Sjors,
> During 2D classification in Relion 1.3 I'm receiving errors such as the one below and the process seems to hang after a few iterations. This happens even though I normalized the particles during particle import step within the Relion GUI. Can you suggest how I might solve the problem? Perhaps relevant is that I'm using K2 movie data that was aligned with IMOD tiltxcorr.
>
> rlnMicrographScaleCorrection= 24918.8 group= 213 my_image_no= 3
> ERROR: rlnMicrographScaleCorrection is very high. Did you normalize your data?
> File: src/ml_optimiser.cpp line: 4321
>
> Thanks,
> Joel
--
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
|