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

diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index 938be0463fd2d28c9a0e58b09e4e7c0fa535ab53..4683fed81684a7bc0aa2204914e27fdfb0c5034e 100644 (file)
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -1263,13 +1263,13 @@ int gmx_chi(int argc, char *argv[])
         "that the dihedral was not in the core region of each rotamer. ",
         "The width of the core region can be set with [TT]-core_rotamer[tt][PAR]",
 
-        "The S^2 order parameters are also output to an [TT].xvg[tt] file",
-        "(argument [TT]-o[tt] ) and optionally as a [TT].pdb[tt] file with",
+        "The S^2 order parameters are also output to an [REF].xvg[ref] file",
+        "(argument [TT]-o[tt] ) and optionally as a [REF].pdb[ref] file with",
         "the S^2 values as B-factor (argument [TT]-p[tt]). ",
         "The total number of rotamer transitions per timestep",
         "(argument [TT]-ot[tt]), the number of transitions per rotamer",
         "(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
-        "can also be written to [TT].xvg[tt] files. Note that the analysis",
+        "can also be written to [REF].xvg[ref] files. Note that the analysis",
         "of rotamer transitions assumes that the supplied trajectory frames",
         "are equally spaced in time.[PAR]",
 
@@ -1340,9 +1340,9 @@ int gmx_chi(int argc, char *argv[])
         { "-normhisto", FALSE, etBOOL, {&bNormHisto},
           "Normalize histograms" },
         { "-ramomega", FALSE, etBOOL, {&bRamOmega},
-          "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [TT].xpm[tt] plot" },
+          "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [REF].xpm[ref] plot" },
         { "-bfact", FALSE, etREAL, {&bfac_init},
-          "B-factor value for [TT].pdb[tt] file for atoms with no calculated dihedral order parameter"},
+          "B-factor value for [REF].pdb[ref] file for atoms with no calculated dihedral order parameter"},
         { "-chi_prod", FALSE, etBOOL, {&bChiProduct},
           "compute a single cumulative rotamer for each residue"},
         { "-HChi", FALSE, etBOOL, {&bHChi},