Hi,
Clearly you are affected by defect lines. What happens if you perform
Class2D with "ignore CTF until first peak: Yes"?
Takanori
On 2021/01/07 18:22, Lora Sinha wrote:
> Hi Takanori,
>
> I did class2d on shiny.star as suggested at the same settings as before (which gave me very good class averages), but I'm not getting the 2d averages
> that I had when I first classified the particles (please see screenshot, the first class has mostly all the particles, the rest out of 100 classes
> have collapsed). I also don't understand this whole issue of hot pixel, could you please elaborate? I did run motion correction in relion 3.1 using
> relion's own implementation. Lastly, the log file of the polishing job showed small unidirectional tracks that are unique to each microgrograph, but
> then I didn't get any increase in resolution after polishing, any comment on that?
>
> On Tue, Jan 5, 2021 at 1:21 PM Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> See https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1907&L=CCPEM&P=R276689
> <https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1907&L=CCPEM&P=R276689>.
>
> If you perform motion correction in RELION 3.1 (but not UCSF MotionCor2),
> defect handling in Polish should be better (but not perfect).
> This is because RELION 3.1's motion correction stores coordinates of detected hot pixels
> and Polish can use it.
>
> Best regards,
>
> Takanori Nakane
>
> On 2021/01/05 18:21, Lora Sinha wrote:
> > After I polished my particles, the reconstruction converged to the same exact resolution that I started with, however, the map that comes from
> > shiny.star now has artifacts that resemble a cat scratch running across the entire particle. Did something go wrong with my polishing job?
> >
> >
> ------------------------------------------------------------------------------------------------------------------------------------------------------
> >
> > To unsubscribe from the CCPEM list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1>
> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1>>
> >
>
>
> ------------------------------------------------------------------------------------------------------------------------------------------------------
>
> To unsubscribe from the CCPEM list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1>
>
########################################################################
To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
|