diff --git a/doc/source/tutorials/basic_usage.rst b/doc/source/tutorials/basic_usage.rst index 2c45776b9..51be9dceb 100644 --- a/doc/source/tutorials/basic_usage.rst +++ b/doc/source/tutorials/basic_usage.rst @@ -54,7 +54,7 @@ User knows best --------------- If you already know the secondary structure of your protein and don't want to worry about -dssp calculating it correctly, the ``-ss`` flag can be used. +dssp assigning it correctly, the ``-ss`` flag can be used instead. The ``-ss`` flag must be one of either: @@ -63,12 +63,21 @@ The ``-ss`` flag must be one of either: For example: -``martinize2 -f 181L_clean.pdb -o t4l_only.top -x t4l_cg.pdb -ss etcetc`` +``martinize2 -f protein.pdb -o topol.top -x cg_protein.pdb -ss HHHHHHHHHH`` -will use the ``etcetc`` dssp formatted string that the user provides to specify how the secondary structure is -treated, which must contain the same number of characters as the residues you have in the protein. +will read the ``HHHHHHHHHH`` dssp formatted string, indicating that there are exactly 10 residues in the +input pdb which should all be treated as part of a helix. If the string provided does not contain the same +number of residues as the input file, an error will be raised. +Alternatively in this case, as we know everything should be a helix, the same result can be achieved through +using a single letter as described above: +``martinize2 -f protein.pdb -o topol.top -x cg_protein.pdb -ss H`` + +If instead we needed to assert that only the first five residues are in a helix, and the final five are coiled, +we must we the full length string again: + +``martinize2 -f protein.pdb -o topol.top -x cg_protein.pdb -ss HHHHHCCCCC`` diff --git a/doc/source/tutorials/elastic_networks.rst b/doc/source/tutorials/elastic_networks.rst index 7922f3375..801003f43 100644 --- a/doc/source/tutorials/elastic_networks.rst +++ b/doc/source/tutorials/elastic_networks.rst @@ -59,14 +59,14 @@ Using decays The strength of the elastic bond can be tuned with distance using an exponential decay function, which uses the ``-ea`` and ``-ep`` flags as input parameters: -.. math:: - decay = e^{(- f * ((x - l) ^p)) + +``decay = exp^{(- f * ((x - l) ^p)}`` where: -- ``l`` = lower bound (-el) -- ``f`` = decay factor (-ea) -- ``p`` = decay power (-ep) +- ``l`` = lower bound (``-el``) +- ``f`` = decay factor (``-ea``) +- ``p`` = decay power (``-ep``) Combining parameters --------------------