Parsing MotionCor2 log files and produce STAR files

Hello everyone, I wonder wether there is a software or script which can help to convert MotionCor2 log into relion star file. In such a way it will be easier to to particle polishing without redoing motion correction in Relion. Thanks!

The best way is to run MC2 with -OutStar 1. Liz Kellogg has some scripts you may be able to adapt but they are in perl.

Hi, Daniel. I ran Motioncor2 (v1.5) command with parameter “-OutStar 1” but there was no any star file created. I wonder whether there are any additional parameters needed to turn on this function. Below shows the command.

MotionCor2_1.5.0_Cuda101_05-31-2022 -InMrc stack_0001.mrc -OutMrc Corsum -InSuffix .mrc -Patch 11 11 20 -Iter 10 -Tol 0.5 -Align 1 -FmRef 1 -Throw 2 -Trunc 0 -Kv 300 -PixSize 0.5 -FmDose 1.61 -FtBin 2 -Gpu 0 1 2 -LogDir ./ -OutAln ./ -OutStar 1

Maybe try -Serial 1.

I think it depends on the format of the micrograph movies? I discussed with Shawn a few months ago regarding MotionCor2’s handling of EER files; it might be on the “to do” list.

Thanks Daniel. Nothing changed after using -Serial 1 parameter.

Do you mean that the star file will only be generated when handling an EER file?

No, the star file is generated for any input. Can you try the most recent version?

It could be related to using -InSuffix, what happens if you don’t?

Also, btw the third number to -Patch doesn’t do anything anymore, -Throw 2 is also very conservative, though maybe reasonable given the very high frame dose. Shawn’s testing showed -Throw 1 could be helpful above 1 e-/Å^2/fm, I’m not sure about 2. Have you tried -InFmMotion?

I also tried the MotionCor2 v.1.6 but it came out with similar result. The command is:

MotionCor2_1.6.3_Cuda101_Feb18_2023 -InMrc stack_0002.mrc -OutMrc Corsum -Patch 11 11 -Iter 10 -Tol 0.5 -Align 1 -FmRef 1 -Throw 1 -Trunc 0 -Kv 300 -PixSize 0.5 -FmDose 1.61 -FtBin 2 -Gpu 0 1 -LogDir ./ -OutAln ./ -OutStar 1

the input and outout are show below: