diff --git a/docs/images/pagina_principal_480p.gif b/docs/images/pagina_principal_480p.gif new file mode 100644 index 0000000..29187f9 Binary files /dev/null and b/docs/images/pagina_principal_480p.gif differ diff --git a/docs/images/pagina_principal_720p.gif b/docs/images/pagina_principal_720p.gif new file mode 100644 index 0000000..19d8e17 Binary files /dev/null and b/docs/images/pagina_principal_720p.gif differ diff --git a/docs/source/About SIRAH.rst b/docs/source/About SIRAH.rst index 751c16d..d5af91c 100644 --- a/docs/source/About SIRAH.rst +++ b/docs/source/About SIRAH.rst @@ -13,7 +13,7 @@ The current version, **SIRAH 2.2**, includes: * A collection of scripts, known as **SIRAH Tools**, that facilitate the process of mapping all-atom files to CG representations, backmapping, visualizing, and analyzing SIRAH trajectories directly on the popular VMD program for molecular visualization. -Pros and cons +Advantages -------------- The SIRAH force field offers several advantages compared to atomistic models in simulating biomolecular systems: @@ -36,6 +36,9 @@ The SIRAH force field offers several advantages compared to atomistic models in **Self-Consistent Force Field**: SIRAH aims to provide a self-consistent force field that describes the intra and intermolecular interactions among moieties of diverse chemical nature in a holistic view of biological ensembles' structural and dynamic features. This ensures that the force field is capable of accurately representing the interactions within biomolecular systems. +Limitations +-------------- + However, it is important to note that the SIRAH force field also has limitations compared to atomistic models: .. image:: ../images/cons.png diff --git a/docs/source/SIRAHTools/Tutorial-tcl.rst b/docs/source/SIRAHTools/Tutorial-tcl.rst index 746bc13..4d17e34 100644 --- a/docs/source/SIRAHTools/Tutorial-tcl.rst +++ b/docs/source/SIRAHTools/Tutorial-tcl.rst @@ -565,6 +565,6 @@ This script will load the topology ``5YWS_cg.psf``, the trajectory ``5YWS_cg_md_ vmd -dispdev text -e sirah_dispdev.tcl -.. tip:: +.. seealso:: - You can find additional information on VMD command-line options `here `__ and available text mode features `here `__. \ No newline at end of file + You can find additional information on VMD command-line options `here `__ and available text mode features `here `__. diff --git a/docs/source/index.rst b/docs/source/index.rst index c851b2e..40efc97 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -10,7 +10,7 @@ Welcome to SIRAH FF documentation **This website is currently undergoing construction, which means that some of its components are constantly being updated and expanded upon.** -.. image:: ../images/pagina_principal.gif +.. image:: ../images/pagina_principal_720p.gif :width: 100%