[phenixbb] FSC curves
pafonine at lbl.gov
Fri Mar 19 15:21:13 PDT 2021
> After running phenix real space refine with different refinement
> strategies. My map-model FSC curve has some interesting features:
> 1. It does not starts at 1 as it does the map FSC curve, is that ok?
> What could be causing this?
which one is it? Is it FSC(half_map1, half_map2) or
FSC(experimental_map, model_map) ?
> 1. It has a dip around 5-6Å, this deep can be a bit up or down
> depending the refinement strategy I use, therefore the FSC model
> at 0.5 can cut the resolution at 3.9 or 6 Å. What this deep mean?
> Am I doing something wrong in the refinement?
How different these models are?
> 1. The mask and unmask curves completely overlap, is that ok?
This suggests to me the map is probably already masked or somehow
> 1. Also, my refinement shows a high clash score (15-20), if I change
> the nonbonded_weight parameter from 100 (default) to higher values
> the clash score decreases but the FSC curves gets lower them the
> FSC curve crosses the 0.5 cutoff at 6A.
When it comes to clashscore, generally the lower the better but zero is
not the goal.
Looking at one of screenshots I see you have 2.42% of atoms with
occupancy less than 1. Do you really see partially occupied atoms in 4A
resolution map? Unlikely! So.. please check those out!
I can run more diagnostics for you if you share maps and models
(off-list of course!).
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