Local refinement immediately terminates with error
“RuntimeError: Binary mask detected. Local refinement must be run with a soft mask. Please use Volume Tools to give the mask a soft padded edge, prior to running local refinement.”
The mask is a soft mask with 9A fallof soft padding generated in Chimera.
Using Volume Tools as suggested yields the same error.
If you see this warning then it is likely that the input mask is indeed binary. All masks that are hand-made should be passed through Volume Tools with a nonzero “Soft padding width”. To help us troubleshoot, can you specify exactly which parameters were set in the Volume Tools job that still produced this downstream error?
thanks for the Tip! giving a nonzero value for “Soft padding width” solved the problem.