Saving mask file from filtertool

[huang....@gmail.com]

Hello,

I've been trying to save an appropriate cylinder mask for subtomogram averaging of my membrane proteins, but I believe instead of saving just the mask, I'm saving the masked map instead. I was wondering how I might be able to just save the mask without the map values.

Thank you!

Judy

[Steve Ludtke]

There are several different ways to generate such a map. Which way are you doing it? If you tell us how you are doing it now, I can suggest an alternative...

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[huang....@gmail.com]

Currently, I'm using the filtertool on an initial reference and making a cylinder mask that captures my protein of interest + membrane interest, then just saving the processed map. 

I saw in the Extra tools for tomography page that the mask should contain values between 0 to 1, but when I open my processed map in chimera, the values are not within that range, and multiplying additional maps with the saved file results in very weird maps that erase density that should be present. 

Thanks!

Judy

[Steve Ludtke]

The cylindrical masking processor, as you observed, applies a mask to an existing map, it doesn't replace the map with the mask. To get a maskfile you need to apply the mask to a map containing 1 in all of the pixels instead. This is easily done.

- adjust the settings in e2filtertool using your data as a reference (as you have already done)

- look at the filtertool_default.txt file which should have been created (use 'cat' on linux/mac, or a text editor)

- you should see a line which looks something like this:

--process=mask.cylinder:inner_radius=0.0:outer_radius=100:phicen=14.0:phirange=25.71:phitriangle=True:phitrirange=25.71:zmax=200.0:zmin=128.0:ztriangle=3.0

- run this command:

e2proc3d.py 256:256:256:1 mymask.hdf --process=mask.cylinder:inner...

where 256 is the size of the mask in pixels, and the --process section is copied and pasted from the text file.

The nx:ny:nz:1 syntax in e2proc3d creates a new image of the specified size and initializes it with the specified value. It can be used for a variety of purposes, including mask creation.

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[Judy Huang]

Thank you!! That was very helpful.

Best,

Judy

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