Re: [scipion-users] refinement with unflipped reference

[David M. B. <Dav...@ut...>]

Dmitry,

Handedness information is lost in 2D projection images.  Therefore, when a 3D reconstruction is computed, the choice of hand is arbitrary.  You simply need to flip the handedness to the correct one.  Resolution will not change, only if you had some particles that were assigned a different handedness than other particles.  But, that would not be a function of whether your starting reference had the correct handedness or not.  It would be a function of whether the resolution range of your orientation alignment was appropriate.  For example, at very low resolutions, handedness cannot be distinguished.  At the high resolutions of many of today’s 3D reconstructions, one can set handedness by looking at the hand of alpha-helices or even individual amino acids if the resolution is high enough.  Handedness also can be determined by doing a tilting experiment.  Here are a couple older articles about tilt experiments that might be helpful:

https://pubmed.ncbi.nlm.nih.gov/9356290/
https://pubmed.ncbi.nlm.nih.gov/14568533/

David


From: "Dmitry A. Semchonok" <sem...@gm...>
Reply-To: Mailing list for Scipion users <sci...@li...>
Date: Monday, July 12, 2021 at 4:13 AM
To: "sci...@li..." <sci...@li...>
Subject: [scipion-users] refinement with unflipped reference

Dear colleagues,

Small theoretical question.

After the 3D refinement it is appeared that the reference needed to be flipped.
Do I need to redo the refinement with flipped reference?
In general, do the processing with wrong hand reference decrease the resolution or the result is just the same?
And why?

Thank you

Sincerely,
Dmitry