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Subject:

Helical reconstruction in Relion 2.1

From:

Sadeem <[log in to unmask]>

Reply-To:

Sadeem <[log in to unmask]>

Date:

Tue, 22 May 2018 20:09:49 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (35 lines)

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

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