Recent changes to AreaPerLipid

AreaPerLipid modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Mon, 12 Nov 2018 21:04:20 -0000

--- v29
+++ v30
@@ -3,7 +3,8 @@
 The Area per Lipid tool calculates both the total area per lipid and the area per lipid of each lipid species of the membrane under analysis. To this end, it uses a user-customizable selection of one key atom (i.e. sterols) or a triad of atoms (i.e. phospho- or sphingolipids). The x and y coordinates of the selected set of points are projected onto a plane delimited by the simulation box. This plane is subsequently divided into polygons through a Voronoi diagram using the program qvoronoi program, from the Qhull package (Barber et al.1996). Thereby, the area of each polygon is calculated.

 ##1. Requirements
-This tool assumes that the membrane under analysis is a continuous plane (e.g. no membrane pores or significant empty spaces) and that the simulations is aligned to the Z axis.
+This tool assumes that the membrane under analysis is a continuous plane (e.g. no membrane pores or significant empty spaces) and that the simulations is aligned to the Z axis. 
+Assignments of lipids to either leaflet is based on which side of the bilayer's center of mass they happen to be. Make sure the lipids are properly wrapped in the Z direction. Extremly deformed membranes may lead also to leaflet assignment issues. Incorrect leaflet assigments may affect obtaned results. 

 Also, see [General Requirements](GeneralRequirements).

AreaPerLipid modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Thu, 18 Jan 2018 21:06:18 -0000

AreaPerLipid modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Wed, 26 Feb 2014 15:43:19 -0000

--- v27
+++ v28
@@ -20,11 +20,8 @@
 * __qvoronoi bynary path__: path to the qhull binary. [See detailed installation instructions](https://sourceforge.net/p/membplugin/wiki/AreaPerLipid/attachment/INSTALL.txt)

-##3. Tutorial

-(Work in progress)
-
-##4. Output file format (tabulated)
+##3. Output file format (tabulated)

 _filename_\_average.area

AreaPerLipid modified by Ramon Guixa

Ramon Guixa — Fri, 13 Dec 2013 00:22:34 -0000

--- v26
+++ v27
@@ -1,9 +1,6 @@
 #Area per lipid tool

-The Area per Lipid tool calculates both the total area per lipid and the area per lipid of each lipid species of the membrane under analysis. To this end, it uses a usercustomizable
-selection of one key atom (i.e. sterols) or a triad of atoms (i.e. phospho- or sphingolipids). The x and y coordinates of the former set of points are projected onto a
-plane delimited by the simulation box which is subsequently divided into polygons through a Voronoi diagram using the program qvoronoi from the Qhull package (Barber et al.
-1996). Thereby, the area of each polygon is calculated.
+The Area per Lipid tool calculates both the total area per lipid and the area per lipid of each lipid species of the membrane under analysis. To this end, it uses a user-customizable selection of one key atom (i.e. sterols) or a triad of atoms (i.e. phospho- or sphingolipids). The x and y coordinates of the selected set of points are projected onto a plane delimited by the simulation box. This plane is subsequently divided into polygons through a Voronoi diagram using the program qvoronoi program, from the Qhull package (Barber et al.1996). Thereby, the area of each polygon is calculated.

 ##1. Requirements
 This tool assumes that the membrane under analysis is a continuous plane (e.g. no membrane pores or significant empty spaces) and that the simulations is aligned to the Z axis.

AreaPerLipid modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Thu, 28 Nov 2013 17:39:04 -0000

--- v25
+++ v26
@@ -76,7 +76,7 @@
 * __Lipid__: residue name of each lipid species.
 * __Area__: average area per lipid of each lipid species.
 * __ResN__: number of residues of each lipid species.
-* __STD\_Error__: standard error of each average area per lipid.
+* __STD\_Error__: standard error of each average area per lipid. In plot versus frames, SE is the average intragrupal standard error inside each frame. 
 * __Frame__: frame number.
 * __Leaflet__: “0” and “1” correspond to upper and bottom leaflets respectively.
 * __MembArea__: average area per lipid of all lipid species (simulation box face area / total number of lipids).

AreaPerLipid modified by Toni

Toni — Mon, 18 Nov 2013 09:46:03 -0000

AreaPerLipid modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Wed, 13 Nov 2013 16:13:11 -0000

--- v23
+++ v24
@@ -20,7 +20,7 @@
 * __To__: last frame number.
 * __Step__:  "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
 * __Output file path__: path to the output files, namely "_filename_\_average.area" containing lipid species averages and "_filename_\_total.area" that contains the total average area per lipid.
-* __qvoronoi bynary path__: path to the qhull binary. ![See detailed installation instructions](https://sourceforge.net/p/membplugin/wiki/AreaPerLipid/attachment/INSTALL.txt)
+* __qvoronoi bynary path__: path to the qhull binary. [See detailed installation instructions](https://sourceforge.net/p/membplugin/wiki/AreaPerLipid/attachment/INSTALL.txt)

 ##3. Tutorial

AreaPerLipid modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Wed, 13 Nov 2013 16:12:34 -0000

--- v22
+++ v23
@@ -20,7 +20,7 @@
 * __To__: last frame number.
 * __Step__:  "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
 * __Output file path__: path to the output files, namely "_filename_\_average.area" containing lipid species averages and "_filename_\_total.area" that contains the total average area per lipid.
-* __qvoronoi bynary path__: path to the qhull binary. [[See detailed installation instructions](INSTALL.txt)]
+* __qvoronoi bynary path__: path to the qhull binary. ![See detailed installation instructions](https://sourceforge.net/p/membplugin/wiki/AreaPerLipid/attachment/INSTALL.txt)

 ##3. Tutorial

AreaPerLipid modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Wed, 13 Nov 2013 16:09:51 -0000

--- v21
+++ v22
@@ -20,7 +20,7 @@
 * __To__: last frame number.
 * __Step__:  "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
 * __Output file path__: path to the output files, namely "_filename_\_average.area" containing lipid species averages and "_filename_\_total.area" that contains the total average area per lipid.
-* __qvoronoi bynary path__: path to the qhull binary. [See detailed installation instructions](INSTALL.txt)
+* __qvoronoi bynary path__: path to the qhull binary. [[See detailed installation instructions](INSTALL.txt)]

 ##3. Tutorial

AreaPerLipid modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Wed, 13 Nov 2013 16:09:11 -0000

--- v20
+++ v21
@@ -20,7 +20,7 @@
 * __To__: last frame number.
 * __Step__:  "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
 * __Output file path__: path to the output files, namely "_filename_\_average.area" containing lipid species averages and "_filename_\_total.area" that contains the total average area per lipid.
-* __qvoronoi bynary path__: path to the qhull binary. [See detailed installation instructions](https://sourceforge.net/p/membplugin/code/ci/master/tree/INSTALL.txt)
+* __qvoronoi bynary path__: path to the qhull binary. [See detailed installation instructions](INSTALL.txt)

 ##3. Tutorial