no real changes, only minor tweaks and comments

examples/maskcheck.py

@@ -2,6 +2,8 @@
 # Reads a mask, reads a coordinate file, and checks how the mask compares
 # with a bulk solvent mask for the coordinate file.
 
+# To check if we produce identical maps as Refmac, use tools/compare_mask.sh.
+#
 # To check if we produce identical maps as cctbx, do:
 #   cctbx.python -m mmtbx.command_line.mask file.pdb
 #   maskcheck.py mask.ccp4 file.pdb

include/gemmi/dencalc.hpp

@@ -187,6 +187,7 @@ struct DensityCalculator {
     if (spacing > 0)
       grid.set_size_from_spacing(spacing, GridSizeRounding::Up);
     else if (grid.point_count() > 0)
+      // d_min not set, but a custom grid has been setup by the user
       grid.fill(0.);
     else
       fail("initialize_grid(): d_min is not set");

prog/sfcalc.cpp

@@ -237,12 +237,11 @@ void process_with_fft(const gemmi::Structure& st,
     fprintf(stderr, "Preparing electron density on a grid...\n");
     fflush(stderr);
   }
-  Timer timer(true);
+  Timer timer(verbose);
   timer.start();
   dencalc.set_grid_cell_and_spacegroup(st);
   dencalc.put_model_density_on_grid(st.models[0]);
-  if (verbose)
-    timer.print("...took");
+  timer.print("...took");
   if (map_file) {
     gemmi::Ccp4<Real> ccp4;
     ccp4.grid = dencalc.grid;

tests/test_prog.py

@@ -88,8 +88,8 @@ def test_sfcalc4(self):
     @unittest.skipIf(sys.platform == 'win32', 'with MSVC it differs slightly')
     def test_sfcalc_5wkd(self):
         self.do('''\
-$ gemmi sfcalc --blur=12 --dmin=2.5 --rate=2.5 --rcut=1e-7 --test -v tests/5wkd.pdb
-[...] 71 87
+$ gemmi sfcalc --blur=12 --dmin=2.5 --rate=2.5 --rcut=1e-7 --test tests/5wkd.pdb
+[...] 65 81
  (-3 1 5)	  52.06	  52.061 	 92.51	 92.510	d= 2.51
  (-2 0 1)	 150.22	 150.220 	360.00	360.000	d=13.74
  (-2 0 2)	  28.77	  28.772 	180.00	180.000	d= 7.34