[3dem] Particle picking within Relion 1.3 using projection images

Sjors Scheres scheres at mrc-lmb.cam.ac.uk
Wed Sep 17 08:30:57 PDT 2014

Dear Marcus,
If you want to make your own references from projections of 3D maps, you 
should use relion_project to do so.
It is very important that you use a 3D reconstruction that you made in 
RELION to make these projections.
relion-project is not accessible from the GUI, type in the command 
without options to see the available options.
PS: These technical RELION_related questions are normally sent to the 
ccpem list.

On 09/17/2014 04:22 PM, mf2944 at columbia.edu wrote:
> Dear all,
> I recently tried using the particle picking within Relion and if I use 
> the recommended procedure doing first a small 2D classification, 
> followed by autopick, the program works fine.
> However, if I make a 2D classification from a few micrographs, the 2D 
> classes are only representing some major orientations that I have in 
> my sample. But for the more rare orientations (those I would 
> especially like to pick more efficiently) I do not obtain a 2D class. 
> These only come up if I make a complete 2D classification using all 
> micrographs.
> Therefore I though to use 2D projections from an initial lower 
> resolution volume I obtained using Relion.
> To create these projections i used xmipp
> xmipp_image_convert -i xxx.mrc -o xxx.vol -t vol
> xmipp_angular_project_library -i xxx.vol -o projection.mrc --sym x 
> --sampling_rate 22.5
> Since the pixel size of the input is twice as big as the pixel size of 
> the new dataset I am working is rescaled the projections
> xmipp_image_resize -i projection.mrc -o projection_scaled.mrc --factor 2
> However, using these as input in the relion particle picking is not 
> successful.
> My feeling is that the FOM for the true particles in the picking are 
> very low.
> As additional information I calculated the statistics of the reference 
> images create in 2D classification vs xmipp projection
> projections
> Total number of images/volumes: 13
> min= -0.912874 max=  2.861991 avg=  0.022331 stddev=  0.633817
> 2D classes
> Total number of images/volumes: 10
> min= -0.481988 max=  0.763749 avg=  0.055558 stddev=  0.249007
> Could anybody help me out with what I could do to get this working? Or 
> am I missing something essential that this route will never work?
> Best regards
> Marcus

Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061

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