Hi Tim,
It seems that apply_mask doesn't set the pixel size correctly in the MRC header of the output map. In Chimera, or any other program that trusts the MRC header, it leads to extremely tiny pixel sizes. Possibly it also contributes to Frealign 9.11 not working well with apply_mask vs. apply_mask.exe (I have a custom apply_mask.com adapted to apply_mask), but I'm not sure. The root issue is XLEN, YLEN, ZLEN being set to 1.0 instead of the extent of the box in Angstroms.
Best,
-da
Hi Daniel,
Thanks for reporting this! This is fixed in our development version, and so will be fixed in the next release.
Until that is out, as a work around, you can use the reset_mrc_header cisTEM command line program to set the pixel size.
Thanks!
Tim