Is the hydration layer not used outside of fitting?
I'm attempting to generate purely a theoretical saxs profile with no fitting. I noticed in the output and in the manual, it doesn't appear that the hydration layer is taken into account in FOXS when it comes to no fitting. The only options are to set ranges, but again, these are only used for fitting. I'm looking for something similar to crysol where you can indicate the solvent density exactly even without fitting.
On 2/1/23 11:12 AM, sammahdi1994--- via IMP-users wrote: > I'm attempting to generate purely a theoretical saxs profile with no > fitting. I noticed in the output and in the manual, it doesn't appear > that the hydration layer is taken into account in FOXS when it comes > to no fitting.
You are correct - the hydration layer parameters are optimized during fitting.
Ben
I've noticed in the FOXS online server, when fitting, you can fix c1 and c2. However, when looking at the CLI --help, you can only set the ranges. --min_c1 arg (=0.99) min c1 value --max_c1 arg (=1.05) max c1 value --min_c2 arg (=-2.00) min c2 value --max_c2 arg (=4.00) max c2 value
How can you fix c1 and c2 to certain values within the CLI?
On 2/5/23 12:59 PM, sammahdi1994--- via IMP-users wrote: > I've noticed in the FOXS online server, when fitting, you can fix c1 > and c2. However, when looking at the CLI --help, you can only set the > ranges. > --min_c1 arg (=0.99) min c1 value > --max_c1 arg (=1.05) max c1 value > --min_c2 arg (=-2.00) min c2 value > --max_c2 arg (=4.00) max c2 value > > How can you fix c1 and c2 to certain values within the CLI?
Just set the min and max to the same value. This is also what the FoXS web server does when it runs the command line tool: https://github.com/salilab/foxs/blob/d98589b6afd/backend/foxs/run_foxs.py#L6...
Ben
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