Replace more [BR] with rst bullet lists

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

diff --git a/src/gromacs/gmxana/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
index 29bab90a0742011d98fa6721915146a4c5585ea7..17c4f392f460a0d943bdc42e3e55effd98c0c4bd 100644 (file)
--- a/src/gromacs/gmxana/gmx_helix.c
+++ b/src/gromacs/gmxana/gmx_helix.c
@@ -67,29 +67,29 @@ int gmx_helix(int argc, char *argv[])
         "hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles.",
         "That bit is fitted",
         "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[GRK]alpha[grk] atoms.",
-        "it is calculated as [SQRT]([SUM][sum][SUB]i[sub] (x^2(i)+y^2(i)))/N[sqrt] 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 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 [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",
-        "number of helical residues (see below).[BR]",
-        "[BB]5.[bb] Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
-        "[BB]6.[bb] RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
-        "atoms only (file [TT]rms-ahx.xvg[tt]).[BR]",
-        "[BB]7.[bb] Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
-        "[BB]8.[bb] Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).[BR]",
-        "[BB]9.[bb] Ellipticity at 222 nm according to Hirst and Brooks.",
-        "[PAR]"
+        "Then the following properties are computed:",
+        "",
+        " * Helix radius (file [TT]radius.xvg[tt]). This is merely the",
+        "   RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.",
+        "   it is calculated as [SQRT]([SUM][sum][SUB]i[sub] (x^2(i)+y^2(i)))/N[sqrt] where N is the number",
+        "   of backbone atoms. For an ideal helix the radius is 0.23 nm.",
+        " * Twist (file [TT]twist.xvg[tt]). The average helical angle per",
+        "   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.",
+        " * Rise per residue (file [TT]rise.xvg[tt]). The helical rise per",
+        "   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.",
+        " * 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",
+        "   number of helical residues (see below).",
+        " * Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).",
+        " * RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
+        "   atoms only (file [TT]rms-ahx.xvg[tt]).",
+        " * Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).",
+        " * Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).",
+        " * Ellipticity at 222 nm according to Hirst and Brooks."
     };
     static gmx_bool    bCheck = FALSE, bFit = TRUE, bDBG = FALSE, bEV = FALSE;
     static int         rStart = 0, rEnd = 0, r0 = 1;