Read EMDB segmentation file format

[Tom Goddard]

The EMDB has developed a segmentation file format for researchers to deposit segmentations. It is called EMDB-SFF and can be read and written by PyPi library sfftk-rw. It is developed by Paul Korir.

Allow ChimeraX to read and display these segmentations.

[Tom Goddard]

I started work on this in October 2019 and recommended several changes to the file format which were made around January 2020.

ChimeraX 1.0 can currently read index map segmentations in EMDB SFF format.

[Tom Goddard]

Still need to test file reader on surface segmentations. This worked in early versions of the library in late 2019 but there were no example files after the format changed in incompatible ways. Paul Korir provided a couple test files at sfftk-rw github

​https://github.com/emdb-empiar/sfftk-rw/tree/master/sfftkrw/test_data/sff/v0.8

Begin forwarded message:

From: Paul Korir
Subject: Re: [Segtrans-wg] Announcement: sfftk for EMDB-SFF v0.8.0.dev1
Date: July 2, 2020 at 5:49:52 AM PDT
To: Tom Goddard
Cc: segtrans-wg@…

Hi Tom,

I'm very sorry for the late reply. I'm only seeing this now.

I've added two files to the test_data folder in the master branch of the repository: one for emd_3971 with meshes and another generic file with shapes. Please let me if they suit your test cases.

For older files with meshes use sfftk-migrate (install with pip install sfftk-migrate) to convert older files to the latest schema.

There should also be some test files with meshes (e.g. from Amira and STL in the sfftk repository i.e. github.com/emdb-empiar/sfftk).

If I don't respond within two days feel free to write to me directly ;-)

Kind regards,

Paul K. Korir, PhD
3D Visualisation Lead
CS3DB
EMBL-EBI

[Elaine Meng]

Isn't this done now? Change log says June 16, 2020 "open EMDB segmentation file format (.sff, .hff) files"

[Tom Goddard]

Still needs testing on surface segmentations. Not sure if EMDB is going to drop this effort. I have not seen any segmentations deposited at EMDB. First step would be to see if any files have been deposited. If not, then probably not worth doing further work on it.