More minor formatting/editorial fixes for the manual.

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

diff --git a/src/tools/gmx_editconf.c b/src/tools/gmx_editconf.c
index f69dc98c203269cd40583871a987e80cce9ae00c..d48947d9cd927fb09a381daf2075016b54fd4877 100644 (file)
--- a/src/tools/gmx_editconf.c
+++ b/src/tools/gmx_editconf.c
@@ -507,7 +507,8 @@ 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, this may allow you to decrease the box volume,",
+                "coordinate axes, with the longest axis aligned with the x 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",
@@ -515,11 +516,11 @@ int gmx_editconf(int argc, char *argv[])
                 "[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",
                 "factor -1 is given in one dimension, one obtains a mirror image,",
-                "mirrored in one of the plains, when one uses -1 in three dimensions",
+                "mirrored in one of the planes. When one uses -1 in three dimensions, ",
                 "a point-mirror image is obtained.[PAR]",
                 "Groups are selected after all operations have been applied.[PAR]",
                 "Periodicity can be removed in a crude manner.",
-                "It is important that the box sizes at the bottom of your input file",
+                "It is important that the box vectors at the bottom of your input file",
                 "are correct when the periodicity is to be removed.",
                 "[PAR]",
                 "When writing [TT].pdb[tt] files, B-factors can be",
@@ -533,24 +534,24 @@ int gmx_editconf(int argc, char *argv[])
                 "a row of CA atoms with B-factors ranging from the minimum to the",
                 "maximum value found, effectively making a legend for viewing.",
                 "[PAR]",
-                "With the option -mead a special pdb (pqr) file for the MEAD electrostatics",
+                "With the option [TT]-mead[tt] a special pdb (pqr) file for the MEAD electrostatics",
                 "program (Poisson-Boltzmann solver) can be made. A further prerequisite",
                 "is that the input file is a run input file.",
                 "The B-factor field is then filled with the Van der Waals radius",
                 "of the atoms while the occupancy field will hold the charge.",
                 "[PAR]",
-                "The option -grasp is similar, but it puts the charges in the B-factor",
+                "The option [TT]-grasp[tt] is similar, but it puts the charges in the B-factor",
                 "and the radius in the occupancy.",
                 "[PAR]",
                 "Option [TT]-align[tt] allows alignment",
                 "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] editconf can add a chain identifier",
+                "Finally with option [TT]-label[tt], editconf can add a chain identifier",
                 "to a pdb file, which can be useful for analysis with e.g. rasmol.",
-                    "[PAR]",
+                "[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]",
+                "a cubic box with the corners cut off (such as GROMOS), use:[BR]",
                 "[TT]editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out>[tt][BR]",
                 "where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2." };
     const char *bugs[] =