ResMap and Frealign
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Hi Everyone!
I am trying to determine the local resolution of my final map using the ResMap tool. This requires the input of two halfvolumes. Can I in principal use the halfvolumes in the scratch folder (3D reconstruction halfset 1 and 2)? What do I need to consider when doing this?
When I inspect these in chimera (e.g. at step 8), i get several parallel density layers spanning the volume of the entire spherical mask. I can only see my particle when I filter very harshly. And even then the map looks very strange (like geographical contour lines).
My final volume reaches a resolution of 6.8 A with ~10k particles
I tried changeing the res_reconstruction from Nyquist closer to my final resolution without any changes.
Thank you!
Yes, you should be able to
Yes, you should be able to use the two maps in the scratch volume for input in ResMap. However, your reconstruction does not look right. I assume the combined map also looks like this. Something must have gone wrong. If you converted angles from a different program, please check your conversion. Another possibility is that there is a strongly preferred orientation of your particle.
Thank you for the swift
In reply to Yes, you should be able to by niko
Thank you for the swift response!
My final map looks fine. The particle is a 60S subunit, which in my experience usually have some slight orientational bias but it should not be a problem (I also calculated this particle with spider and relion).
Thanks!
Maybe this helps:
# Computer-specific setting
cluster_type sge
nprocessor_ref 61
nprocessor_rec 50
mem_per_cpu 2048
# Refinement-specific parameters
MODE 1
start_process 2
end_process 2
res_high_refinement 10.0
res_high_class 8.0
nclasses 1
DANG 200.0
ITMAX 200
# Dataset-specific parameters
data_input params
raw_images stack
image_contrast N
outer_radius 200.0
inner_radius 0.0
mol_mass 2000.0
Symmetry C1
pix_size 2.168
dstep 28.0
Aberration 2.7
Voltage 300.0
Amp_contrast 0.1
# Expert parameters (for expert users)
XSTD 0.0
PBC 2.0
parameter_mask "1 1 1 1 1"
refineangleinc 1
refineshiftinc 1
res_reconstruction 4.336
res_low_refinement 0.0
thresh_reconst 22.0
thresh_refine 50.0
nbootstrap 1000
FMAG F
FDEF F
FASTIG F
FPART F
FFILT T
FMATCH F
FBEAUT F
FBOOST F
RBfactor 0.0
beam_tilt_x 0.0
beam_tilt_y 0.0
mp_cpus 4
restart_after_crash F
delete_scratch T
first_particle
last_particle
frealign_bin_dir
scratch_dir
# Masking parameters (for expert users)
mask_file
mask_edge 5
mask_outside_weight 0.0
mask_filt_res 0.0
mask_filt_edge 5
In that case it might just be
In reply to Thank you for the swift by lukater
In that case it might just be a high-resolution artifact. The two half maps in scratch are not filtered in any way and therefore any interpolation artifacts that might occur near Nyquist (where one usually does not trust the reconstruction) will affect the map. If filtering restores reasonably looking maps, this is what you should do.