I have 4 maps that have 0.143 cutoffs of between 2.2-2.6 A, and Nyquist was ~2.1 A. Using an old version of cryosparc we ran local resolution with DeepRes enabled, which gave me a resolution range from 2.1-3.5 A on our 2.2 A map, which looked great. However, now running local resolution method on cryosparc (w/o deep res because I don’t see the option for it anymore) that same 2.2 A map gets masked to 2.3 A, with essentially the entire map being 2.3 A (one color) when I color using Chimera.
When I run my other maps which are lower resolution than this one the lowest Res on histogram is still 2.3 A, and they keep getting masked to around 2.3 A. Is 2.3 A some sort of lower limit for the new method without DeepRes? Additionally, does anyone know if there is any way to use deep res local resolution in crypsparc still?
Thanks for the post, and welcome to the forum . Could you let us know:
what parameter corresponds to the “DeepRes” option, and
if possible, which older CryoSPARC version was used for the local resolution job where this was enabled?
We aren’t immediately familiar with which parameter the DeepRes option corresponds to in our local resolution job.
For the main issue, could you also let us know the status of the “Cap local resolution estimate” parameter in the local resolution job? This parameter effectively thresholds all local resolution values that are better than the Global FSC resolution, and brings them up to this value, which may explain the effect you’re seeing. If this parameter is off though, then this wouldn’t explain it. As well, it is odd that all other lower-resolution maps also are capped at 2.3Å – for each of the local resolution jobs run, could you reply with the “Global FSC” plot that is written to the event log? These plots would show us the 0.143 threshold value that would be used for this capping procedure.
Regarding the visualization issue, the local resolution histogram shown in your post looks fairly healthy with a reasonable distribution of values, but visualization can often be misleading depending on the colormap. Chimera’s colormap that maps local resolution values to colours may need to be specified exactly as outlined in this post. Can you try this and let us know if the map looks reasonable?