Dear Yangqi,

The 4.7A repeat was sometimes at a slightly different z-height in the
map (as both half-maps were independently refined from a common low-pass
filtered reference). This kept the structure from progressing to higher
resolutions. We used UCSF chimera, Fit in map, and the 'vop resample
onGrid' to align the half2 map onto the half1 map. Note this was always
a small translation along Z (of less than 4.7/2A). We then overwrote the
original half2 map with the aligned one, and restarted relion-refine
using the --continue option from the iteration where we had modified the
position of the half2 map. 

HTH,

Sjors



On 01/31/2019 03:18 AM, BuddySphinx wrote:
>
> Hi Dan,
>
> Thank you for your answer. I am still a bit of confused. Did they
> manually shift the map and save the consensus? In that case, do we
> need to cut out the consensus? I am not sure how it translates to the
> particles? Do they just shift the particles by a certain amount of the
> distance belongs to one of the half map?
>
> Best,
>
> Yangqi
>
>  
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>  
>
> *From: *Daniel Asarnow <mailto:[log in to unmask]>
> *Sent: *Wednesday, January 30, 2019 7:50 PM
> *To: *Yangqi Gu <mailto:[log in to unmask]>
> *Cc: *[log in to unmask] <mailto:[log in to unmask]>
> *Subject: *Re: [ccpem] Alignment of helical particles outside RELION
>
>  
>
> I think the references became shifted somehow, so they just aligned
> the maps in chimera and saved the results as new references, to keep
> everything together in the box. One could also transform the particles
> the same way, so the shifts can continue to be locally aligned.
>
>  
>
> Best,
>
> -da
>
>  
>
> On Wed, Jan 30, 2019 at 3:18 PM Yangqi Gu <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear all,
> I was reading 2017 nature paper "Fitzpatrick, Anthony WP, et al.
> "Cryo-EM structures of tau filaments from Alzheimer’s disease." Nature
> 547.7662 (2017): 185.". In their methods, they mentioned additional
> alignment before final refinement "In some refinements, the two
> half-maps converged
> onto different translations along the helical axis. In such cases, it
> was necessary to halt the run and align the two half-maps outside
> RELION, before resuming the refinement." I am wondering if someone
> could explain to me how they did this? What program did they use and
> what did they do? What was the cause and why additional alignment
> would help? Thank you.
> Yangqi
>
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-- 
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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