Differences

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--- fourier_maps [2020/07/13 12:37] – created johnsoevans
+++ fourier_maps [2025/09/19 15:18] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
+====== Fourier Maps in Superflip ======
+In addition to the TOPAS Fourier map calculations and viewer, you can output information to calculate/view maps in other software.
+The macro below was contributed by Lynne McCusker.  It creates an input file for superflip to calculate an (Fobs-Fcalc) difference map.  This can be output in a format (.xplor) that can be read by Chimera or Vesta.  It can be executed with a simple "superflip file.inflip" command.  The file.inflip will need minor editting to remove the quotation marks around the symmetry operators.
+<code topas>
+macro Out_Inflip(file)
+' Prints a superflip input file to generate a difference Fourier map in xplor format'
+' that can be viewed in Chimera'
+' The command  'superflip file' will then produce a diffmap_phasename.xplor file'
+{
+	out file
+	Out_String("title superflip difference map")
+	Out(Get(phase_name), " %s")
+	Out_String("\n\ndimension 3")
+	Out_String("\nvoxel 112 56 40")
+	Out_String("\ncell")
+	Out(Get(a), " %10.5f")
+   	Out(Get(b), " %10.5f")
+   	Out(Get(c), " %10.5f")
+   	Out(Get(al), " %10.5f")
+   	Out(Get(be), " %10.5f")
+   	Out(Get(ga), " %10.5f")
+   	Out_String("\n\ncenters")
+   	Out_String("\n 0 0 0")
+   	Out_String("\nendcenters")
+   	Out_String("\n\nsymmetry")
+   	Out(Get(sp_xyzs_txt),  "%s")
+   	Out_String("\nendsymmetry")
+   	Out_String("\n\nperform fourier")
+   	Out_String("\nterminal yes")
+   	Out(Get(phase_name), "\n\noutputfile diffmap%s.xplor")
+   	Out_String("\noutputformat xplor")
+   	Out_String("\n\ndataformat a b")
+   	Out_String("\nfbegin")
+ 	phase_out file append load out_record out_fmt out_eqn
+ 	{
+	"\n%4.0f" = H;
+	"%4.0f"   = K;
+	"%4.0f"   = L;
+ 	"%15.4f"  = ((A01-B11)/Sqrt((A01-B11)^2+(B01+A11)^2)) * (Sqrt(Iobs_no_scale_pks/(M*Get(scale))) - Sqrt((A01-B11)^2+(B01+A11)^2));  'A Fdiff'
+ 	"%15.4f"  = ((B01+A11)/Sqrt((A01-B11)^2+(B01+A11)^2)) * (Sqrt(Iobs_no_scale_pks/(M*Get(scale))) - Sqrt((A01-B11)^2+(B01+A11)^2));  'B Fdiff'
+ 	}
+        out file append
+	Out_String("\nendf")
+}
+</code>