Thanks for the heads up! Does this mean I should process only the non-magnification anisotropy corrected images or that I can process with them, but when I perform particle polishing I wont be able to apply the correction? In other words, should I redo the alignment without magnification anisotropy correction and work with that data, or can I work with magnification anisotropy corrected images without issues up until particle polishing? Thanks for all the help!
Colin Deniston
UCSD Graduate Student
Chemistry and Biochemistry Department
________________________________
From: Takanori Nakane <[log in to unmask]>
Sent: Monday, September 10, 2018 11:55:49 AM
To: Colin K Deniston; [log in to unmask]
Subject: Re: [ccpem] Relion 3.0 MotionCor2 Commands
Hi Colin,
You should put '-Mag x y z' to the "Other MOTIONCOR2 arguments" box
in the "Motion" tab, not the "Additional arguments" box in the
"Running" tab.
The command line to MotionCor2 and its output are written in
(subdirectories of) the job directory as <micrograph_name>.com and
<micrograph_name>.out, respectively.
Note that RELION 3.0 does NOT support anisotropic magnification
correction. This means that the shiny particles after Bayesian
Polishing revert to an uncorrected state. We understand this is a
problem, but the refinement and correction of anisotropic
magnification will be in 3.1, not 3.0.
Best regards,
Takanori Nakane
On 2018/09/10 18:12, Colin K Deniston wrote:
> Hello all,
>
>
> I'm a graduate student running MotionCor2 through the new Relion 3.0 GUI and I wish to run with an additional MotionCor2 input for magnification anisotropy ("-Mag x y z"). I can not tell if Relion is actually passing the command through and if MotionCor2 is using the input values. I have tried adding "-Mag x y z" and "--other_motioncor2_args -Mag x y z" in the additional arguments box in the Relion GUI, however I can not tell from any of the files in the output whether Relion successfully passed the command along. Relion has also output "The following warnings were encountered upon command-line parsing: WARNING: Option -Mag is not a valid RELION argument" both times. Any help in correcting how I input the command and/or where I can look to see that the command was actually passed through to MotionCor2 would be greatly appreciated. Thanks!
>
>
> Colin Deniston
> UCSD Graduate Student
> Chemistry and Biochemistry Department
>
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