Oliver Clarke

Hi, I'm attempting to install this on CentOS but running into the attached error - any thoughts? Cheers Oli ``` user@c112384:~/software/OmegaFold$ pip install -r requirements.txt Exception: Traceback (most recent call...

Hi, when using relion_display, it would be great to have the option to overlay a mask, just showing the binarization threshold. This would be useful when running remotely, where it...

Check parameters before execution

1

Hi, some parameters provided to relion_refine are only checked for validity after the first iteration. This is annoying when the first iteration is long (hrs). For example, unlike many other...

support for TF2/CUDA 11?

25

Hi, We have a new GPU with RTX-3090s, which require CUDA 11.1 or later. Will DeepEMhancer work on this system? I am assuming not because it uses CUDA 10/TF 1...

Request - show nearby residues when selecting residue in Ramachandran plot

3

Hi Paul, when navigating the main Ramachandran plot interface, clicking on a residue recenters on that residue. It would be useful if there were a way to then see just...

Hi, Symmetry relaxation (--relax_sym) works if I start a fresh 3D-auto-refine job in relion 5-beta, but if I continue that same refinement (e.g. after replacing the mask), it gives the...

--relax_sym argument is ignored when continuing jobs, and is not available when image alignment is disabled

5

Hi, The option to relax symmetry (`--relax_sym`) is respected when starting a new run, but when continuing an old run it is ignored ("not a valid relion argument"), even when...

`add_module_restraints()` generates old version of restraints menu

1

Hi Paul, In 0.9.8.92, the API versions of the "add module" commands (e.g. `add_module_restraints()`) launch old versions of the corresponding menus, compared to what the corresponding Calculate...Modules menu items do...

NCS with multi-chain master?

1

Hi Paul, It would be useful to be able to set the NCS master to a multi-chain selection, to deal with cases where the asymmetric unit is comprised of multiple...

Assigning two models to auto-update maps generates an infinite loop

2

See screen recording using tutorial model and data: https://www.dropbox.com/scl/fi/ubw2ymr3dn9utds1ysy8x/one_infinite_loop.mov?rlkey=52t1efjklu69jvzd2tz2vhq84&dl=0 Basically, if two models are assigned to update the map, Coot goes into an infinite loop of calculating & recalculating maps....