Tons of small fixes to documentation.

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

diff --git a/src/tools/gmx_editconf.c b/src/tools/gmx_editconf.c
index 89702eb8901714a8f8f7b022f478cb387f37eb54..3662585b71abc74a999c76e3d5e2581d1f37abb1 100644 (file)
--- a/src/tools/gmx_editconf.c
+++ b/src/tools/gmx_editconf.c
@@ -485,20 +485,21 @@ int gmx_editconf(int argc, char *argv[])
                 "The last two are special cases of a triclinic box.",
                 "The length of the three box vectors of the truncated octahedron is the",
                 "shortest distance between two opposite hexagons.",
-                "The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
-                "is 0.77 of that of a cubic box with the same periodic image distance.",
+                "Relative to a cubic box with some periodic image distance, the volume of a ",
+                "dodecahedron with this same periodic distance is 0.71 times that of the cube, ",
+                "and that of a truncated octahedron is 0.77 times.",
                 "[PAR]",
                 "Option [TT]-box[tt] requires only",
-                "one value for a cubic box, dodecahedron and a truncated octahedron.",
+                "one value for a cubic, rhombic dodecahedral, or truncated octahedral box.",
                 "[PAR]",
-                "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
-                "and z directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
+                "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the [IT]x[it]-, [IT]y[it]-,",
+                "and [IT]z[it]-directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
                 "[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
                 "to the diameter of the system (largest distance between atoms) plus twice",
                 "the specified distance.",
                 "[PAR]",
                 "Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
-                "a triclinic box and can not be used with option [TT]-d[tt].",
+                "a triclinic box and cannot be used with option [TT]-d[tt].",
                 "[PAR]",
                 "When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
                 "can be selected for calculating the size and the geometric center,",
@@ -507,14 +508,14 @@ int gmx_editconf(int argc, char *argv[])
                 "[TT]-rotate[tt] rotates the coordinates and velocities.",
                 "[PAR]",
                 "[TT]-princ[tt] aligns the principal axes of the system along the",
-                "coordinate axes, with the longest axis aligned with the x axis. ",
+                "coordinate axes, with the longest axis aligned with the [IT]x[it]-axis. ",
                 "This may allow you to decrease the box volume,",
                 "but beware that molecules can rotate significantly in a nanosecond.",
                 "[PAR]",
                 "Scaling is applied before any of the other operations are",
                 "performed. Boxes and coordinates can be scaled to give a certain density (option",
-                "[TT]-density[tt]). Note that this may be inaccurate in case a gro",
-                "file is given as input. A special feature of the scaling option, when the",
+                "[TT]-density[tt]). Note that this may be inaccurate in case a [TT].gro[tt]",
+                "file is given as input. A special feature of the scaling option is that when the",
                 "factor -1 is given in one dimension, one obtains a mirror image,",
                 "mirrored in one of the planes. When one uses -1 in three dimensions, ",
                 "a point-mirror image is obtained.[PAR]",
@@ -548,8 +549,8 @@ int gmx_editconf(int argc, char *argv[])
                 "of the principal axis of a specified group against the given vector, ",
                                "with an optional center of rotation specified by [TT]-aligncenter[tt].",
                 "[PAR]",
-                "Finally with option [TT]-label[tt], [TT]editconf[tt] can add a chain identifier",
-                "to a [TT].pdb[tt] file, which can be useful for analysis with e.g. rasmol.",
+                "Finally, with option [TT]-label[tt], [TT]editconf[tt] can add a chain identifier",
+                "to a [TT].pdb[tt] file, which can be useful for analysis with e.g. Rasmol.",
                 "[PAR]",
                 "To convert a truncated octrahedron file produced by a package which uses",
                 "a cubic box with the corners cut off (such as GROMOS), use:[BR]",