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
Awesome! Thanks!!!
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
Hi Tim
Initially I was not aware of how to use it.But now problem solved.
Thankyou for your help and concern
Tim
Hi
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
Hi
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
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
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
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 just saying why the results may be different.
Tim
Can you post the header of your star file?
Tim
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 your star file that you are trying to import..
Thanks,
Tim
Hi
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
Can someone reply on this.It would be helpful
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
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
Hi Tim
All particles are in one file only.
Priyanka
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 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