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# System prepended metadata

title: Density-guided simulation paper - figure iteration notes

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# Density-guided simulation paper - figure iteration notes


Figure 1
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 - [ ] model density and density under B) look different
 - [ ] move helix with forces closer to flow and make larger
 - [ ] all densities same size
 - [ ] better connection "blue red" funnels to simlarity
 - [ ] make space on left of C, connect to density sim measure rel entropy
 - [ ] connect funnels with dashed lines to potentials

Figure 2
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 - [x] change free energy landscape color scheme to blue-gray-red
 - [x] check if you can reduce text and make text uniform
 - [x] A) make schematic, remove arrow and explain in caption
 - [x] be consistent in capitalisation, centering

Figure 3
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 - [x] A) remove gray box
 - [x] B) up arrow, down arrow
 - [x] C) average force, remve time, reaction coordinate along x,  $<F>$
 - [ ] explain rest in caption


Figure 4
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 - [ ] best fsc average @ 3$\sigma$
 - [ ] legend A can be in figure
 - [ ] B) put up legend
 - [ ] B) rotate label 180
 - [ ] C) goes up too much
 - [ ] density seems to have moved


Figure 5
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 - [ ] think of supplement - all fits same
 - [ ] almost no differences between A-C annoying


Figure 6 
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 - [ ] A distorted
 - [ ] B fitted
 - [ ] Show RMSD
 - [ ] Show FSC (in SI

FIgure 7
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 - [ ] focus on differences for singe time constant
 - [ ] put else in SI


Wrap up?
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 - [ ] FSC? Structure -> simulation -> fscfit
 - [ ] FSC result helix or aldolase as final thing; FSC as function of time
