diff --git a/README.md b/README.md
index beb21f3edd9e12ea66125842775b065d9eb1a799..186b7ab166effa832e83f35121f22615431b8d05 100644
--- a/README.md
+++ b/README.md
@@ -3,19 +3,21 @@
# PyCGTOOL
Please see http://pycgtool.readthedocs.io/en/master/ for full documentation.
-Python reimplementation of [CGTOOL](https://bitbucket.org/jag1g13/cgtool) performing coarse-grain mapping of molecular dynamics trajectories.
-The aim of this project is to provide a tool to aid in parametrising coarse-grained (CG) molecular mechanics models. PyCGTOOL generates coarse-grained models from atomistic trajectories using a user-provided mapping. Equilibrium values and force constants of bonded terms are calculated by Boltzmann Inversion of histograms collected from the input trajectory allowing good replication of target properties.
+A Python program for automated generation of coarse-grained molecular dynamics models from atomistic simulation trajectories.
-Alternatively it may be used in map-only mode (behaving similarly to MARTINIZE) to generate initial coordinates to use with existing CG topologies such as the MARTINI lipid models.
+The aim of this project is to provide a tool to aid in parametrising coarse-grained (CG) molecular mechanics models. PyCGTOOL generates coarse-grained models from atomistic simulation trajectories using a user-provided mapping. Equilibrium values and force constants of bonded terms are calculated by Boltzmann Inversion of bond distributions collected from the input trajectory.
-PyCGTOOL makes it easy to test multiple variations in mapping and bond topology by making simple changes to the config file.
+Alternatively map-only mode (behaving similarly to MARTINIZE) may be used to generate initial coordinates to use with existing CG topologies such as the MARTINI lipid models. For instance, a pre-equilibrated atomistic membrane may be used to create starting coordinates for a MARTINI membrane simulation.
+
+PyCGTOOL makes it easy to test multiple variations in mapping and bond topology by making simple changes to the config files.
This version has several advantages over the original C++ implementation CGTOOL:
* PyCGTOOL is able to run anywhere the necessary library dependencies are available (all available from pip)
* Does not require that residues are present in contiguous sorted blocks
+* May map multiple residues with a single pass
+* Support for polymers such as DNA or proteins making use of GROMACS' pdb2gmx
* Much more automated testing ensures that regressions will be identified quickly
-* Work-in-progress support for polymers such as DNA or proteins making use of GROMACS' pdb2gmx
If you experience problems or wish to see a new feature added please [file an issue](https://github.com/jag1g13/pycgtool/issues).
@@ -39,3 +41,5 @@ PyCGTOOL requires:
The bundled test code may be run using your preferred Python testing frontend although nose is recommended.
All library dependencies may be installed from pip using the command `pip install -r requirements.txt`
+
+This program is a reimplementation of the earlier [CGTOOL](https://bitbucket.org/jag1g13/cgtool).
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 0f246c0a483993f5a4250e51615e3bb3abdc4935..d8c8e316fabfda11c761457ceaf993da0d73ac0d 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -125,7 +125,7 @@ Mapping-only mode performs a coarse-grain mapping on a single frame and may be u
pycgtool.py -g <GRO file> -m <MAP file>
-Measure-only mode may be used to aid in the testing of a coarse-grained model by making measurements of bonds from a true corase-grained simulation trajectory. These bond measurements are those collected from the pseudo-coarse-grained trajectory used to generate the model, so are a directly comparable measure of model accuracy. This mode may be invoked by::
+Measure-only mode may be used to aid in the testing of a coarse-grained model by making measurements of bonds from a true coarse-grained simulation trajectory. These bond measurements may be compared directly to those collected from the pseudo-coarse-grained trajectory used to generate the model. This mode may be invoked by::
pycgtool.py -g <GRO file> -x <XTC file> -b <BND file>
@@ -143,10 +143,10 @@ map_only Run in mapping-only mode **False**, Tru
map_center Mapping method **geom**, mass
constr_threshold Convert stiff bonds to constraints over **100000**, any number
dump_measurements Whether to output bond measurements **False**, True
-dump_n_values How many measurements to output **100000**, any number
+dump_n_values How many measurements to output **10000**, any number
output_forcefield Output a GROMACS forcefield directory? **False**, True
temperature Temperature of reference simulation **310**, any number
-angle_default_fc Default MARTINI force constant on angles? **True**, False
+default_fc Use default MARTINI force constants? **False**, True
generate_angles Generate angles from bonds **True**, False
generate_dihedrals Generate dihedrals from bonds **False**, True
================== ========================================== =======================
diff --git a/doc/source/pycgtool.rst b/doc/source/pycgtool.rst
index a61ef054c4e1ad21403f73b6d45e595c141a3207..4f6aded4de1272c48919e24e4e18eb4a5a95fa78 100644
--- a/doc/source/pycgtool.rst
+++ b/doc/source/pycgtool.rst
@@ -20,7 +20,6 @@ Submodules
pycgtool.mapping
pycgtool.pycgtool
pycgtool.util
- pycgtool.warnings
Module contents
---------------