Exporting the list of Good Images

Hi Tim,

After Find CTF, I examined the images and the CTF Fit, and selected a set of 'good' images.

Is there a way to export the list of these good images that I have slected.

I would like to also try processing in Relion, but do not want to go through all the images again to select the good ones.

Thanks,

Stephen

Hi Stephen,

You can do this by directly accessing the database. This is one of the examples covered in the "images in a group" section here :-

https://cistem.org/documentation#tab-1-16

Thanks,

Tim

Hi Tim,

I am not able to export the good images selected after CTF fit curve.Can you please help for the same.

Hi Priyanka,

Did you try the database commands in the link above? What problem are you seeing?

Thanks,

Tim

reply#5

Hi Tim

Initially I was not aware of how to use it.But now problem solved.

Thankyou for your help and concern

Tim

regarding import of relion stack into cisTEM

Can you please help me how to import the stack from relion to cisTEM.When I am trying to do from refinement package import option, I am facing an error.

Thanks

priyanka

Hi Priyanka,

Is this from Relion 3.1? If so then it won't work as 3.1 is not supported in the released version of cisTEM.

There is some discussion here :-

https://cistem.org/cant-import-relion-31-particles-cistem

You can modify the star file so that it will import, you essentially have to convert it into the old style.

Thanks,

Tim

Hi Tim

Yes, it is from Relion 3. I will try to modify the file.

Thankyou

Tim

regarding alignment of movie file

Can someone please suggest me regarding an issue with movie alignment.I have encountered a difference between the motion corrected micrograph when I am doing alignment of movies in Relion and cisTEM.I have seen that when I am doing motion correction as well as ctf correction both in cisTEM then resolution fit curve is different as compared to when I am using motion corrected micrographs by Relion then doing ctf correction in cisTEM.I know in both the software the algorithm is different so can someone tell me which way I should follow.

It would be really help in data processing.

Thanks

Priyanka

Hi Priyanka,

The alignments will be different, also in cisTEM the default is to use the movies for CTF estimation, if you import images from Relion then it cannot use Movies.

Thanks,

Tim

Reply#8

Hi Tim

I am using Relion 3.0 not Relion 3.1 still I can't import the stack file .Can you please comment on this.

Thanks

Hi Priyanka,

What error are you seeing?

Can you paste the header of the star file here?

Tim

reply#13

Hi Tim

This is the error

home/grigoriefflab/compiled/wxWidgets3_static/include/wx-3.0/wx/strvararg.h(456): assert "(argtype & (wxFormatStringSpecifier<T>::value)) == argtype" failed in wxArgNormalizer(): format specifier doesn't match argument type.

Please suggest me how to tackle it

reply#11

Hi Tim

the alignment wouls be different but in CTF estimation it can take images also.So we can use Relion motioncorrected images.

Yes, this will work - I'm

Yes, this will work - I'm just saying why the results may be different.

Tim

Can you post the header of

Can you post the header of your star file?

Tim

#17

Hi Tim

Sorry to ask but can you please tell what exactly you want me to post

Priyanka

The first 100 lines or so of

The first 100 lines or so of your star file that you are trying to import..

Thanks,

Tim

regarding retracing the particles selected from 2d classes

Can someone suggest me how to retrace the particle position selected after 2d classification.I want to see the selected particles on micrograph itself from which particle belongs to.

Thankyou

Priyanka

reply#20

Can someone reply on this.It would be helpful

reply#19

Hi Tim
This is star file header.

# RELION; version 3.0
data_
loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnClassNumber #3
_rlnAutopickFigureOfMerit #4
_rlnAnglePsi #5
_rlnImageName #6
_rlnMicrographName #7
_rlnMagnification #8
_rlnDetectorPixelSize #9
_rlnCtfMaxResolution #10
_rlnCtfFigureOfMerit #11
_rlnVoltage #12
_rlnDefocusU #13
_rlnDefocusV #14
_rlnDefocusAngle #15
_rlnSphericalAberration #16
_rlnCtfBfactor #17
_rlnCtfScalefactor #18
_rlnPhaseShift #19
_rlnAmplitudeContrast #20
_rlnOriginX #21
_rlnOriginY #22
_rlnGroupNumber #23
_rlnAngleRot #24
_rlnAngleTilt #25
_rlnNormCorrection #26
_rlnLogLikeliContribution #27
_rlnMaxValueProbDistribution #28
_rlnNrOfSignificantSamples #29
_rlnGroupName #30
1963.926503 628.969926 1 1.748691 87.786941 000049@Extract/job027/Stack/20200304_1125_A013_G000_H006_D001.mrcs MotionCorr/job010/Stack/20200304_1125_A013_G000_H006_D001.mrc 10000.000000 1.200000 6.523637 -0.00381 200.000000 24168.191406 22763.585938 11.292921 2.700000 0.000000 1.000000 0.000000 0.100000 -2.72922 -10.72922 1 42.809557 107.624284 0.408273 8612.520438 0.751557 3 group_1

Priyanka

Hi Priyanka,

This looks like a star file for images, not a particle stack. Am I correct. cisTEM will only directly import a particle stack and corresponding star file.

Tim

reply#22

Hi Tim

This is the particles.star file of selected classes after 2d classification.

Hi Priyanka,

Do you have all your particles in a single file, or do you have a different file for the particles from each image?

Tim

Reply#25

Hi Tim

All particles are in one file only.

Priyanka

significance of Alias resolution

Hi,

Can someone please comment on the significance of Alias Resolution parameter shown during CTF estimation.If it is showing NONE then what does that mean?

Is there any relation of this value with Fit resolution?

Thanks,

Regards,

Priyanka

This is the resolution that

This is the resolution that the CTF starts to osicallate every pixel - if it is none it means that does not happen within your resolution range.

In general, this is not something you probably have to worry about.

Tim