cryoet analysis

[hejhlearing]

when i using Extract i want to know whether i get the correct .so i want to know how to judge in paricle.star . and the function of Extract and re-project real subtomo .Thanks for your help

[bogdantoader]

Hello, to visualise the particles in a particles.star, run the Pick tomograms job with Picking mode: particles and your star file in Input particles.star. This will open Napari with your particles annotated on the tomogram. For more details, please see the bottom of this page in the Relion 5 tomo tutorial.

[hejhlearing]

Hello, to visualise the particles in a particles.star, run the Pick tomograms job with Picking mode: particles and your star file in Input particles.star. This will open Napari with your particles annotated on the tomogram. For more details, please see the bottom of this page in the Relion 5 tomo tutorial.

thanks for your help. But i am so confuse that when i take the job ,it says that No such command 'particles-from-star'. i dont know whenther i need to install new version of the software .(i use the beta4) Another question ,i use pytom to template ,but when i do the extract job ,i cant exchange the boxsize it still keep 32pix and bin4 (i want to do bin1)

[bogdantoader]

Yes please use the latest version, there is a relion-5.0.0 stable release now on Github. Please try to extract the pytom particles once you have the stable release and write here if there are still isues.

[hejhlearing]

Yes please use the latest version, there is a relion-5.0.0 stable release now on Github. Please try to extract the pytom particles once you have the stable release and write here if there are still isues.

yes ,i try to use stable version in our hpc .but it still says No such command. and another question is when i use pytom to template picking. i ues bin4 tomography and boxsize 32. but when i extract and Class3d in relion . the boxsize i cant change whatever i keep ,it still keep 32

[hejhlearing]

maybe i need to do bin1 tomography ? when i want to use another software to template

[bogdantoader]

Regarding the error: what version of Relion are you using on the cluster?

Regarding the bin 1 extraction: this is likely unrelated to whether the particles come from pytom or not. What options are you using in the Extract job?

[hejhlearing]

关于错误：您在集群上使用的 Relion 版本是什么？

关于 bin 1 提取：这可能与粒子是否来自 pytom 无关。您在 Extract 作业中使用了哪些选项？

when i take the Extract Job . I use bin1(3.435) and boxsize 128 .and i check the particle.star,it still write by 13.74A/px and 32 boxsize .but when i pick the particles in napari in the pick job it can change the bin when i take the job

[hejhlearing]

关于错误：您在集群上使用的 Relion 版本是什么？

关于 bin 1 提取：这可能与粒子是否来自 pytom 无关。您在 Extract 作业中使用了哪些选项？

and i use the relion5 -stable version .5.0.0

[hejhlearing]

i find that i need to change the parameters mannually. So i think maybe it need to solve by myself in the Extract Job. the question about napari, i will ask the hpc manager more details after the holiday. Thanks