IMOD coordinates for sphere mask

Submitted by AK on Fri, 2016-02-05 07:43

Forums

Frealign

Hi,

I wonder how to tell frealign to use a sphere mask with coordinates read out of IMOD's XYZ module. I cannot find the command 'focus_mask' in the mparameters file. And how do I provide the IMOD coordinates that frealign can read them? I just find the settings for providing an external mask by adding the file name in mparameters.

Best regards,
Alex

niko Fri, 2016-02-05 09:57

Are you running the latest version of Frealign? The keyword 'focus_mask' should be listed in the mparameters file of the latest version.

AK Fri, 2016-02-05 10:30

yes, it's /frealign/9.11

but the mask part looks like this:
# Masking parameters (for expert users)
mask_file
mask_edge 5 ! Width of cosine edge in pixels to add around mask. Set to 0 to leave mask unchanged.
mask_outside_weight 0.0 ! Factor to downweight density outside of mask (normally 0.0 - 1.0).
mask_filt_res 0.0 ! Filter radius (in A) to low-pass filter density outside density. Set to 0.0 to skip filtering.
mask_filt_edge 5 ! Width of cosine edge in reciprocal pixels to add to filter function.

niko Fri, 2016-02-05 11:35

It looks like you did not properly install the new version. Please make sure you follow the installation instructions, including updating the path settings in your login script. Then source this scrip out log out and back in.