[scipion-users] Fwd: relion_localized_reconstruction - weird results

[Pablo C. <pc...@cn...>]

I do not think this made it to the list.

I'm forwarding it on behalf of Stefano.



-------- Forwarded Message --------
Subject: 	relion_localized_reconstruction - weird results
Date: 	Wed, 23 Jan 2019 16:06:37 +0100
From: 	Stefano Trapani <tr...@cb...>
Organisation: 	Centre de Biochimie Structurale
To: 	sci...@li..., CCPEM <CC...@JI...>



Dear all

(sorry if I am sending this message to two mailing lists at the same time)

I am finding some weird results (see the attached picture) after using 
the /relion_localized_reconstruction.py/ procedure described by Ilca et 
al (2015) and implemented in Scipion.

The picture on the left shows the C1 reconstruction of an icosahedral 
virus starting from a set of previously aligned, symmetry-expanded and 
signal-subtracted particles (using RELION 3.0). The reconstructed 
density corresponds to a protein pentamer centred on one of the 5-fold 
symmetry axes (plus some residual signal around the rest of the viral 
particle). The reconstruction box size is 356x356x356 pixels.

The picture on the right shows the reconstruction obtained after 
sub-particle extraction into a smaller box (96x96x96). Sub-particle 
extraction was carried out without realignment in C1 and without signal 
subtraction (for the starting particles had already been 
symmetry-expanded and signal-subtracted; the details of the command 
parameters used are shown in the picture).

Surprisingly, the reconstruction from the extracted sub-particles looks 
significantly different (worse) than the original one (I would expect 
them to be the same within the 96x96x96 box).

Any reason that could explain that? Did I use some wrong parameter ? Is 
this a bug ?

Rem: the alignment angles in the original and sub-particle star files 
seem to be correct (do not know if the same goes for the sub-particle 
origins).

Best regards

-- 
Stefano Trapani

Maître de Conférences
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
-------------------------------------
Centre de Biochimie Structurale (CBS)
29 rue de Navacelles
34090 MONTPELLIER Cedex, France

Tel : +33 (0)4 67 41 77 29
Fax : +33 (0)4 67 41 79 13
-------------------------------------
Université de Montpellier
CNRS UMR 5048
INSERM UMR 1054
-------------------------------------


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