Is there a way to apply two masks? I'd like to use one mask to apply a low-pass filter outside of the mask (say lowpass 10A, weight 1.0) and a second mask, which is larger, to apply a lower weight (weight 0.0).
There isn't really a way to do this directly in the gui I'm afraid.
There is a spherical mask at the radius specified (using mask radius for local searches and global mask radius for global searches) additional to the mask you specify, so perhaps you can use this to kind of achieve what you want.
Two shaped masks can't be applied however. If you wanted to do a nasty "hack", you could use a 3D you had masked yourself (e.g. by running apply_mask from the command line twice sequentially, starting with the structure and using two different masks). The 3D is masked by the gui before the job is launched, and stored in your Scratch/ManualRefine3D directory. If you put your last run profile entry as a single entry with a large delay, you can copy over the version that you want on top of the one the gui puts there after clicking start (you have to wait until the gui has actually done the masking and put the file there), and this will be used for the refinement when it eventually runs. You would have to do this 1 by 1 for every iteration however, so it isn't very nice.
Other than that, You could script a refinement procedure yourself using the command line programs, but this would have to be done outside of the gui.
There isn't really a way to do this directly in the gui I'm afraid.
There is a spherical mask at the radius specified (using mask radius for local searches and global mask radius for global searches) additional to the mask you specify, so perhaps you can use this to kind of achieve what you want.
Two shaped masks can't be applied however. If you wanted to do a nasty "hack", you could use a 3D you had masked yourself (e.g. by running apply_mask from the command line twice sequentially, starting with the structure and using two different masks). The 3D is masked by the gui before the job is launched, and stored in your Scratch/ManualRefine3D directory. If you put your last run profile entry as a single entry with a large delay, you can copy over the version that you want on top of the one the gui puts there after clicking start (you have to wait until the gui has actually done the masking and put the file there), and this will be used for the refinement when it eventually runs. You would have to do this 1 by 1 for every iteration however, so it isn't very nice.
Other than that, You could script a refinement procedure yourself using the command line programs, but this would have to be done outside of the gui.
Cheers,
Tim