Hi Sadeem,
I would run with 1 or 2 new AUs in each box. That way you can deal with
flexibility in the helices better (as explained in Shaoda He's paper).
HTH,
Sjors
> Hi all,
> I have a question regarding helical reconstruction in Relion 2.1. I am
> processing a filament data with a rise of 44A. For a box size of 300 pix
> (1 pix=1.169A), when I am choosing the number of asymmetric units in 3D
> auto-refine equal to 4, I am getting an error message:
>
> helix.cpp::chechParametersFor3DHelicalReconstruction(): Number of
> asymmetrical units exceeds its upper bound!
>
> The central z length is set to 60%. I am confused as to why I am getting
> this error because as I understand:
> Number of asu should be less than (Box size (A) * central z-length) /
> (Helical rise)
> Therefore according to my calculations: ( 300 * 1.169 * 0.6 )/ 44 = 4.78 A
> which should accommodate 4 asu.
>
> What I find surprising is that the program runs smoothly if I choose the
> number of asu= 3 or if I reduce the central z length to 40% without
> changing any other parameter. Any help in this regard would be highly
> appreciated. Also, since I am new to the field, I must apologize in
> advance if there is a lack of understanding or oversight on my part. For
> reference, I have listed below all the relevant parameters from Particle
> Extraction and 3D auto-refine below that return the error message:
>
> Particle Extraction parameters:
> Particle box size = 300 pix
> Rescale particles = No
> Extract helical segments = Yes
> Tube diameter = 100 A
> Co-ordinates are start-to-end only = Yes
> Cut helical tubes into segments = Yes
> Number of asu = 1
> Helical rise = 44 A
>
> Refinement parameters:
> Mask diameter = 260 A
> Helical reconstruction = Yes
> Inner tube diameter = 10 A
> Outer tube diameter = 100 A
> Apply helical symmetry= Yes
> Number of asu = 4
> Initial twist = 80 deg
> Helical rise = 44 A
> Central Z-length = 60%
>
> Thank and best wishes,
> Sadeem
>
--
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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