Tons of small fixes to documentation.

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

diff --git a/src/tools/gmx_helix.c b/src/tools/gmx_helix.c
index 0d55691f1190ae98347af545e7a8d27876ca5d79..ca64bc5596a2a4c0406269e4e65815ac1277fb42 100644 (file)
--- a/src/tools/gmx_helix.c
+++ b/src/tools/gmx_helix.c
@@ -124,21 +124,21 @@ int gmx_helix(int argc,char *argv[])
   const char *desc[] = {
     "[TT]g_helix[tt] computes all kinds of helix properties. First, the peptide",
     "is checked to find the longest helical part, as determined by",
-    "hydrogen bonds and Phi/Psi angles.",
+    "hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles.",
     "That bit is fitted",
-    "to an ideal helix around the Z-axis and centered around the origin.",
+    "to an ideal helix around the [IT]z[it]-axis and centered around the origin.",
     "Then the following properties are computed:[PAR]",
     "[BB]1.[bb] Helix radius (file [TT]radius.xvg[tt]). This is merely the",
-    "RMS deviation in two dimensions for all C-alpha atoms.",
+    "RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.",
     "it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number",
     "of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
     "[BB]2.[bb] Twist (file [TT]twist.xvg[tt]). The average helical angle per",
-    "residue is calculated. For alpha helix it is 100 degrees,",
-    "for 3-10 helices it will be smaller,", 
+    "residue is calculated. For an [GRK]alpha[grk]-helix it is 100 degrees,",
+    "for 3-10 helices it will be smaller, and ", 
     "for 5-helices it will be larger.[BR]",
     "[BB]3.[bb] Rise per residue (file [TT]rise.xvg[tt]). The helical rise per", 
-    "residue is plotted as the difference in Z-coordinate between Ca", 
-    "atoms. For an ideal helix this is 0.15 nm[BR]",
+    "residue is plotted as the difference in [IT]z[it]-coordinate between C[GRK]alpha[grk]", 
+    "atoms. For an ideal helix, this is 0.15 nm[BR]",
     "[BB]4.[bb] Total helix length (file [TT]len-ahx.xvg[tt]). The total length", 
     "of the", 
     "helix in nm. This is simply the average rise (see above) times the",  
@@ -146,10 +146,10 @@ int gmx_helix(int argc,char *argv[])
     "[BB]5.[bb] Number of helical residues (file [TT]n-ahx.xvg[tt]). The title says",
     "it all.[BR]",
     "[BB]6.[bb] Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
-    "[BB]7.[bb] RMS deviation from ideal helix, calculated for the C-alpha",
+    "[BB]7.[bb] RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
     "atoms only (file [TT]rms-ahx.xvg[tt]).[BR]",
-    "[BB]8.[bb] Average C-alpha - C-alpha dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
-    "[BB]9.[bb] Average Phi and Psi angles (file [TT]phipsi.xvg[tt]).[BR]",
+    "[BB]8.[bb] Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
+    "[BB]9.[bb] Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).[BR]",
     "[BB]10.[bb] Ellipticity at 222 nm according to Hirst and Brooks.",
     "[PAR]"
   };