Tons of small fixes to documentation.

[alexxy/gromacs.git] / src / tools / gmx_helixorient.c

diff --git a/src/tools/gmx_helixorient.c b/src/tools/gmx_helixorient.c
index 2ea8af35006141748a373b5f7fc1483cd1732ed4..973d9d293f1b20d4afda60f8dc695f787eaac79e 100644 (file)
--- a/src/tools/gmx_helixorient.c
+++ b/src/tools/gmx_helixorient.c
@@ -60,17 +60,17 @@ int gmx_helixorient(int argc,char *argv[])
   const char *desc[] = {
     "[TT]g_helixorient[tt] calculates the coordinates and direction of the average",
     "axis inside an alpha helix, and the direction/vectors of both the",
-    "alpha carbon and (optionally) a sidechain atom relative to the axis.[PAR]",
-    "As input, you need to specify an index group with alpha carbon atoms",
-    "corresponding to an alpha helix of continuous residues. Sidechain",
+    "C[GRK]alpha[grk] and (optionally) a sidechain atom relative to the axis.[PAR]",
+    "As input, you need to specify an index group with C[GRK]alpha[grk] atoms",
+    "corresponding to an [GRK]alpha[grk]-helix of continuous residues. Sidechain",
     "directions require a second index group of the same size, containing",
     "the heavy atom in each residue that should represent the sidechain.[PAR]",
-    "Note that this program does not do any fitting of structures.[PAR]",
-    "We need four C-alpha coordinates to define the local direction of the helix",
+    "[BB]Note[bb] that this program does not do any fitting of structures.[PAR]",
+    "We need four C[GRK]alpha[grk] coordinates to define the local direction of the helix",
     "axis.[PAR]",
     "The tilt/rotation is calculated from Euler rotations, where we define",
-    "the helix axis as the local X axis, the residues/CA-vector as Y, and the",
-    "Z axis from their cross product. We use the Euler Y-Z-X rotation, meaning",
+    "the helix axis as the local [IT]x[it]-axis, the residues/C[GRK]alpha[grk] vector as [IT]y[it], and the",
+    "[IT]z[it]-axis from their cross product. We use the Euler Y-Z-X rotation, meaning",
     "we first tilt the helix axis (1) around and (2) orthogonal to the residues",
     "vector, and finally apply the (3) rotation around it. For debugging or other",
     "purposes, we also write out the actual Euler rotation angles as [TT]theta[1-3].xvg[tt]"