I have run flexible refinement and I can see improvements on the appearance of certain loops in my map. However, the downsampling has caused a decrease in the resolution of other parts of the map. What would be the best way to perform flex reconstruction with the non cropped particles and maintaining the Flex Train parameters?
Please can you provide addtitional details:
- At what box size did you perform 3D Flex reconstruction?
- What is the “non cropped” particles’ box size?
- Was a real-space crop also applied do get from “non cropped particles” to the particles used in 3D Flex reconstruction?
Hello,
Please see bellow the answers to the questions. Thank you so much for taking a look at this.
- At what box size did you perform 3D Flex reconstruction? 320
- What is the “non cropped” particles’ box size? 640
- Was a real-space crop also applied do get from “non cropped particles” to the particles used in 3D Flex reconstruction? Yes, to 256 before a downsampling to 128 on the Flex prep step.
Thanks for these details @joana.paulino
Was 320 px the box size of the input particles in the 3D Flex Data Prep job?
Were the input particles for 3D Flex Data Prep prepared with a Downsample Particles job with 640 px box size particle input? If so, what were the values of the parameters (please indicate if left blank/default)
- Crop / pad to box size
- Desired approx. pixel size (A)
- Fourier crop to box size (pix)
Did you specify 256 for Crop box size (px) in the 3D Flex Data Prep job, or another value?