I used the cluster mode in 3DVA to separate different conformations of my protein.
But the density of the motion/flexible region is still badly resolved and the model cannot be properly builded.
I’ve tried low-pass filter between 5 to 15 A when running 3DVA.
However, that region still cannot be resolved clearly enough to do the model building.
Also the local refinement didn’t work.
I used the same number of low-pass filter for 3DVA and 3DVA display.
Will it help, for example, low-pass filter at 10 A for 3DVA and display without low-pass filter ?
Generally, should the low-pass filter be the same for 3DVA and 3DVA display?
Because the region accounts for nearly half of my protein, I cannot just ignore that region during model building.
Is there any suggestion?
All the best,