Merge pull request #52 from luciannahss/lu-sirah-doc

Tutot_analy_index_mod
SIRAHFF · Oct 30, 2023 · 6be55b0 · 6be55b0
2 parents c4951d9 + 45817d7
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diff --git a/docs/images/pagina_principal_480p.gif b/docs/images/pagina_principal_480p.gif
diff --git a/docs/images/pagina_principal_720p.gif b/docs/images/pagina_principal_720p.gif
diff --git 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
@@ -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 <https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.7/ug/node204.html>`__ and available text mode features `here <https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node8.html>`__.
+   You can find additional information on VMD command-line options `here <https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.7/ug/node204.html>`__ and available text mode features `here <https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node8.html>`__.
diff --git 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%