simple transformation of a star file

[P C]

Is there a tool to shift origins of a species by a specified vector (no rotation, just a shift) within Warp/M tools? If yes, Is it possible to combine multiple species into one and filter for duplicates?

All these problems could be solved if I could export M star file back to Relion star file. But it seems that there is no easy way back. 

[Alister Burt]

Hey, separate species are supposed to be different objects so combining them doesn’t make much sense, I guess you’re working with some kind of lattice and treating different symmetry axes as different species?

For shifting you have https://warpem.github.io/warp/reference/mtools/api/mtools/#shift_species

Sent from mobile - apologies for brevity

On Oct 8, 2025, at 18:37, P C <peter.p.c...@gmail.com> wrote:



Is there a tool to shift origins of a species by a specified vector (no rotation, just a shift) within Warp/M tools? If yes, Is it possible to combine multiple species into one and filter for duplicates?

All these problems could be solved if I could export M star file back to Relion star file. But it seems that there is no easy way back. 

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[P C]

Thank you, this is very useful. I was not aware of these tools! 

In my case, subtomograms are chunks of a semi-regular lattice. The reconstruction allows me to define new subsets of subtomograms in the vicinity, which belong to the same species. So, adding (shifted) particles to an existing species would be a useful feature at least in this project. I went back to the initial extracted subtomos that were refined in relion, and expanded the relion star file, combined, filtered for duplicates etc with relion_star_handler.  It then required a little bit of troubleshooting to extract the expanded set of particles (ts_export_particles  does not understand fully formatted relion star files; and minimally one needs to remove optics header and add _rlnDetectorPixelSize column, which confusingly must be not the original but the binned pixel size), but it worked very well. 

Peter

[Alister Burt]

Hi Peter,

Probably best to just manipulate your input star file before import into M, here is my script containing particle recenter/reorient logic (written for recentering, you would need to expose reorienting to the CLI if you wanted that too)

https://gist.github.com/alisterburt/8744accf3f4696dd6d83fc9c4690612c

Cheers,

Alister

Sent from mobile - apologies for brevity

On Oct 9, 2025, at 15:07, P C <peter.p.c...@gmail.com> wrote:



To view this discussion visit https://groups.google.com/d/msgid/warp-em/b3ec8eb1-181a-478d-a3b6-dd0714279f41n%40googlegroups.com.