Dear RELION tomo developers and users,
I have a question regarding "Remove duplicates"function in relion4.0-beta invoked with "--tomo" option:
When trying to remove duplicates for a tomography data set,
> + Using the provided pixel size for original micrographs before extraction: 2.07
> + The minimum inter-particle distance 150 A corresponds to 72.4638 px in the micrograph coordinate (rlnCoordinateX/Y).
> + The particle shifts (rlnOriginXAngst, rlnOriginYAngst) are multiplied by 0.483092 to bring it to the same scale as rlnCoordinateX/Y.
> Removed 5 duplicated objects from 735 objects.
> Written: Select/job034/particles.star
> Done!
the message only indicates that it is removing particles that are too close in the X/Y plane. Is it also taking into account Z coordinates?
Looking at removeDuplicatedParticles(), this appears to be the case, but I would appreciate if anyone has confirmed it or have an idea.
https://github.com/3dem/relion/blob/master/src/metadata_table.cpp
Thank you and best regards,
Yongchan
--
Yongchan Lee, PhD
Assistant Professor
New Address:
Laboratory of Biological Membrane Dynamics
Graduate School of Medical Life Science
Yokohama City University
1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa, 230-0045, Japan
E-mail: [log in to unmask]
Old Address:
Department of Structural Biology, Max Planck Institute of Biophysics
Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
E-mail: [log in to unmask]
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