Hi Pranav,
Or relion_image_handler can be used with --threshold_above and
--threshold_below for the same result. Use relion_image_handler --stats
to see whether it's the min or the max vaklue (or both).
HTH,
Sjors
On 01/11/2018 11:55 PM, Ludtke, Steven J wrote:
> Is it possible that there was a small roundoff error of some sort when you ran the processor. You could try using the threshold.binary, or the threshold.clampminmax processors to insure the final output is in the desired range.
> --------------------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Charles C. Bell Jr., Professor of Structural Biology
> Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
> Co-Director CIBR Center (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)
> Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu<http://ncmi.bcm.edu>)
> Baylor College of Medicine
> [log in to unmask]<mailto:[log in to unmask]>
>
> On Jan 11, 2018, at 5:20 PM, Pranav Shah <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> I want to run 3D classification of my viral particles based on the capsid features and not that genome. To that end, I created a mask in eman using e2filtertool.py and flipped the intesities such that the solvent is 0 the capsid is 1 and the genome is 0. When this mask is provided, the 3D classification step aborts after the first iteration with the following error
>
> MlOptimiser::solventFlatten: ERROR solvent mask should contain values between 0 and 1 only...
> File: /software/relion/relion/src/ml_optimiser.cpp line: 3893
>
> I would appreciate your help on continuing from this step.
>
> Looking forward to hearing from you.
>
> Best,
> Pranav
> --
> Pranav Shah
>
>
>
--
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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