From 222c87b77f17a099c4b908ab23fe19ad93a249dc Mon Sep 17 00:00:00 2001 From: Justin Lemkul Date: Tue, 22 Mar 2011 10:55:40 -0400 Subject: [PATCH] Lots of editorial fixes to descriptions, etc. to make the manual a bit cleaner and more consistent. --- src/kernel/gmxdump.c | 2 +- src/kernel/grompp.c | 6 +++--- src/tools/do_dssp.c | 2 +- src/tools/gmx_genpr.c | 4 ++-- src/tools/gmx_helix.c | 16 ++++++++-------- src/tools/gmx_helixorient.c | 2 +- src/tools/gmx_membed.c | 22 +++++++++++----------- src/tools/gmx_nmeig.c | 14 +++++++------- src/tools/gmx_rms.c | 6 +++--- src/tools/gmx_rmsdist.c | 2 +- 10 files changed, 38 insertions(+), 38 deletions(-) diff --git a/src/kernel/gmxdump.c b/src/kernel/gmxdump.c index 7cda183986..4e99088d84 100644 --- a/src/kernel/gmxdump.c +++ b/src/kernel/gmxdump.c @@ -466,7 +466,7 @@ int main(int argc,char *argv[]) "This program is essential for checking your run input file in case of", "problems.[PAR]", "The program can also preprocess a topology to help finding problems.", - "Note that currently setting GMXLIB is the only way to customize", + "Note that currently setting [TT]GMXLIB[tt] is the only way to customize", "directories used for searching include files.", }; t_filenm fnm[] = { diff --git a/src/kernel/grompp.c b/src/kernel/grompp.c index a987b5037f..005a6e063c 100644 --- a/src/kernel/grompp.c +++ b/src/kernel/grompp.c @@ -1152,8 +1152,8 @@ int main (int argc, char *argv[]) "Note that the atom names are irrelevant for the simulation as", "only the atom types are used for generating interaction parameters.[PAR]", - "[TT]grompp[tt] uses a built-in preprocessor to resolve includes, macros ", - "etcetera. The preprocessor supports the following keywords:[BR]", + "[TT]grompp[tt] uses a built-in preprocessor to resolve includes, macros, ", + "etc. The preprocessor supports the following keywords:[BR]", "#ifdef VARIABLE[BR]", "#ifndef VARIABLE[BR]", "#else[BR]", @@ -1163,7 +1163,7 @@ int main (int argc, char *argv[]) "#include \"filename\"[BR]", "#include [BR]", "The functioning of these statements in your topology may be modulated by", - "using the following two flags in your [TT]mdp[tt] file:[BR]", + "using the following two flags in your [TT].mdp[tt] file:[BR]", "define = -DVARIABLE1 -DVARIABLE2[BR]", "include = -I/home/john/doe[BR]", "For further information a C-programming textbook may help you out.", diff --git a/src/tools/do_dssp.c b/src/tools/do_dssp.c index 2789dfb0e2..6a1faaac57 100644 --- a/src/tools/do_dssp.c +++ b/src/tools/do_dssp.c @@ -390,7 +390,7 @@ int main(int argc,char *argv[]) "calling the dssp program. If you do not have the dssp program,", "get it. [TT]do_dssp[tt] assumes that the dssp executable is", "/usr/local/bin/dssp. If this is not the case, then you should", - "set an environment variable [BB]DSSP[bb] pointing to the dssp", + "set an environment variable [TT]DSSP[tt] pointing to the dssp", "executable, e.g.: [PAR]", "[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]", "The structure assignment for each residue and time is written to an", diff --git a/src/tools/gmx_genpr.c b/src/tools/gmx_genpr.c index e55e961843..db91ea7447 100644 --- a/src/tools/gmx_genpr.c +++ b/src/tools/gmx_genpr.c @@ -63,8 +63,8 @@ int gmx_genpr(int argc,char *argv[]) "they should be included within the correct [TT][ moleculetype ][tt]", "block in the topology. Since the atom numbers in every moleculetype", "in the topology start at 1 and the numbers in the input file for", - "genpr number consecutively from 1, genpr will only produce a useful", - "file for the first molecule.[PAR]", + "[TT]genrestr[tt] number consecutively from 1, [TT]genrestr[tt] will only", + "produce a useful file for the first molecule.[PAR]", "The [TT]-of[tt] option produces an index file that can be used for", "freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]", "With the [TT]-disre[tt] option, half a matrix of distance restraints", diff --git a/src/tools/gmx_helix.c b/src/tools/gmx_helix.c index 45bbbc3471..0d55691f11 100644 --- a/src/tools/gmx_helix.c +++ b/src/tools/gmx_helix.c @@ -122,14 +122,14 @@ void dump_otrj(FILE *otrj,int natoms,atom_id all_index[],rvec x[], int gmx_helix(int argc,char *argv[]) { const char *desc[] = { - "[TT]g_helix[tt] computes all kind of helix properties. First, the peptide", - "is checked to find the longest helical part. This is determined by", - "Hydrogen bonds and Phi/Psi angles.", + "[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.", "That bit is fitted", "to an ideal helix around the Z-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 Calpha atoms.", + "RMS deviation in two dimensions for all C-alpha 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", @@ -145,12 +145,12 @@ int gmx_helix(int argc,char *argv[]) "number of helical residues (see below).[BR]", "[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 Calpha", + "[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", "atoms only (file [TT]rms-ahx.xvg[tt]).[BR]", - "[BB]8.[bb] Average Calpha-Calpha dihedral angle (file [TT]phi-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]10.[bb] Ellipticity at 222 nm according to [IT]Hirst and Brooks[it]", + "[BB]10.[bb] Ellipticity at 222 nm according to Hirst and Brooks.", "[PAR]" }; static const char *ppp[efhNR+2] = { diff --git a/src/tools/gmx_helixorient.c b/src/tools/gmx_helixorient.c index 60e6636655..2ea8af3500 100644 --- a/src/tools/gmx_helixorient.c +++ b/src/tools/gmx_helixorient.c @@ -66,7 +66,7 @@ int gmx_helixorient(int argc,char *argv[]) "directions require a second index group of the same size, containing", "the heavy atom in each residue that should represent the sidechain.[PAR]", "Note that this program does not do any fitting of structures.[PAR]", - "We need four Calpha coordinates to define the local direction of the helix", + "We need four C-alpha coordinates to define the local direction of the helix", "axis.[PAR]", "The tilt/rotation is calculated from Euler rotations, where we define", "the helix axis as the local X axis, the residues/CA-vector as Y, and the", diff --git a/src/tools/gmx_membed.c b/src/tools/gmx_membed.c index 2b573bdb98..ddbb528746 100644 --- a/src/tools/gmx_membed.c +++ b/src/tools/gmx_membed.c @@ -4303,25 +4303,25 @@ int gmx_membed(int argc,char *argv[]) "\n", "SHORT METHOD DESCRIPTION\n", "------------------------\n", - "1. The protein is resized around its center of mass by a factor -xy in the xy-plane", - "(the membrane plane) and a factor -z in the z-direction (if the size of the", + "1. The protein is resized around its center of mass by a factor [TT]-xy[tt] in the xy-plane", + "(the membrane plane) and a factor [TT]-z[tt] in the z-direction (if the size of the", "protein in the z-direction is the same or smaller than the width of the membrane, a", - "-z value larger than 1 can prevent that the protein will be enveloped by the lipids).\n", + "[TT]-z[tt] value larger than 1 can prevent that the protein will be enveloped by the lipids).\n", "2. All lipid and solvent molecules overlapping with the resized protein are removed. All", - "intraprotein interactions are turned off to prevent numerical issues for small values of -xy", - " or -z\n", + "intraprotein interactions are turned off to prevent numerical issues for small values of [TT]-xy[tt]", + " or [TT]-z[tt]\n", "3. One md step is performed.\n", - "4. The resize factor (-xy or -z) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the", + "4. The resize factor ([TT]-xy[tt] or [TT]-z[tt]) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the", "protein is resized again around its center of mass. The resize factor for the xy-plane", - "is incremented first. The resize factor for the z-direction is not changed until the -xy factor", - "is 1 (thus after -nxy iteration).\n", - "5. Repeat step 3 and 4 until the protein reaches its original size (-nxy + -nz iterations).\n", - "For a more extensive method descrition see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.\n", + "is incremented first. The resize factor for the z-direction is not changed until the [TT]-xy[tt] factor", + "is 1 (thus after [TT]-nxy[tt] iterations).\n", + "5. Repeat step 3 and 4 until the protein reaches its original size ([TT]-nxy[tt] + [TT]-nz[tt] iterations).\n", + "For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.\n", "\n", "NOTE\n----\n", " - Protein can be any molecule you want to insert in the membrane.\n", " - It is recommended to perform a short equilibration run after the embedding", - "(see Wolf et al, J Comp Chem 31 (2010) 2169-2174, to re-equilibrate the membrane. Clearly", + "(see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly", "protein equilibration might require longer.\n", "\n" }; diff --git a/src/tools/gmx_nmeig.c b/src/tools/gmx_nmeig.c index e547e04922..428561f5bb 100644 --- a/src/tools/gmx_nmeig.c +++ b/src/tools/gmx_nmeig.c @@ -271,15 +271,15 @@ int gmx_nmeig(int argc,char *argv[]) "manual chapter 1 for details. The result includes subtracting a harmonic", "degree of freedom at the given temperature.", "The total correction is printed on the terminal screen.", - "The recommended way of getting the corrections out is:", - "g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr]", - "The constr should be used when bond constraints were used during the", + "The recommended way of getting the corrections out is:[PAR]", + "[TT]g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr][tt][PAR]", + "The [TT]-constr[tt] option should be used when bond constraints were used during the", "simulation [BB]for all the covalent bonds[bb]. If this is not the case", - "you need to analyse the quant_corr.xvg file yourself.[PAR]", - "To make things more flexible, the program can also take vsites into account", + "you need to analyse the [TT]quant_corr.xvg[tt] file yourself.[PAR]", + "To make things more flexible, the program can also take virtual sites into account", "when computing quantum corrections. When selecting [TT]-constr[tt] and", - "[TT]-qc[tt] the [TT]-begin[tt] and [TT]-end[tt] options will be set automatically as well.", - "Again, if you think you know it better, please check the eigenfreq.xvg", + "[TT]-qc[tt], the [TT]-begin[tt] and [TT]-end[tt] options will be set automatically as well.", + "Again, if you think you know it better, please check the [TT]eigenfreq.xvg[tt]", "output." }; diff --git a/src/tools/gmx_rms.c b/src/tools/gmx_rms.c index a363bb4a29..98090c8a84 100644 --- a/src/tools/gmx_rms.c +++ b/src/tools/gmx_rms.c @@ -124,9 +124,9 @@ int gmx_rms(int argc, char *argv[]) "Option [TT]-mw[tt] controls whether mass weighting is done or not.", "If you select the option (default) and ", "supply a valid [TT].tpr[tt] file masses will be taken from there, ", - "otherwise the masses will be deduced from the atommass.dat file in", - "the GROMACS library directory. This is fine for proteins but not", - "necessarily for other molecules. A default mass of 12.011 amu (Carbon)", + "otherwise the masses will be deduced from the [TT]atommass.dat[tt] file in", + "[TT]GMXLIB[tt]. This is fine for proteins, but not", + "necessarily for other molecules. A default mass of 12.011 amu (carbon)", "is assigned to unknown atoms. You can check whether this happend by", "turning on the [TT]-debug[tt] flag and inspecting the log file.[PAR]", diff --git a/src/tools/gmx_rmsdist.c b/src/tools/gmx_rmsdist.c index db20963e7b..93e0d6a241 100644 --- a/src/tools/gmx_rmsdist.c +++ b/src/tools/gmx_rmsdist.c @@ -513,7 +513,7 @@ int gmx_rmsdist (int argc,char *argv[]) "which has the advantage that no fit is needed like in standard RMS", "deviation as computed by [TT]g_rms[tt].", "The reference structure is taken from the structure file.", - "The rmsd at time t is calculated as the rms", + "The RMSD at time t is calculated as the RMS", "of the differences in distance between atom-pairs in the reference", "structure and the structure at time t.[PAR]", "[TT]g_rmsdist[tt] can also produce matrices of the rms distances, rms distances", -- 2.22.0