Recent changes to ScdOrderParameter

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Tue, 27 Mar 2018 18:43:04 -0000

--- v37
+++ v38
@@ -12,7 +12,7 @@

 1. __Atom selection__: atom selection that set the residues (see Resnames at [GUIMainwindow]) to be analyzed. Sterols must be not selected. __Default__: “not resname CHL1”.
 * __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. 
-If more than one chain is selected, average of carbons with the same assigned index will be shown instead in the generated plot (but not in the .dat file). 
+If more than one chain is selected, average of carbons with the same assigned index will be shown instead in the generated plot (but not in the .orderparSCD file). 
 __Important Note__:  lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
 * __Leaflets__: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "-SCD vs Frame" plot.
 * __From__: initial frame number.

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Tue, 27 Mar 2018 18:41:33 -0000

--- v36
+++ v37
@@ -12,7 +12,7 @@

 1. __Atom selection__: atom selection that set the residues (see Resnames at [GUIMainwindow]) to be analyzed. Sterols must be not selected. __Default__: “not resname CHL1”.
 * __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. 
-If more than one chain is selected, average of carbons with the same assigned index will be shown instead in the generated plot (but not in the .dat file ) 
+If more than one chain is selected, average of carbons with the same assigned index will be shown instead in the generated plot (but not in the .dat file). 
 __Important Note__:  lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
 * __Leaflets__: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "-SCD vs Frame" plot.
 * __From__: initial frame number.

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Tue, 27 Mar 2018 18:40:26 -0000

--- v35
+++ v36
@@ -12,7 +12,7 @@

 1. __Atom selection__: atom selection that set the residues (see Resnames at [GUIMainwindow]) to be analyzed. Sterols must be not selected. __Default__: “not resname CHL1”.
 * __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. 
-If more than one chain is selected, average of carbons with the same assigned index will be shown in the generated plot (but not in the .dat file ) 
+If more than one chain is selected, average of carbons with the same assigned index will be shown instead in the generated plot (but not in the .dat file ) 
 __Important Note__:  lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
 * __Leaflets__: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "-SCD vs Frame" plot.
 * __From__: initial frame number.

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Tue, 27 Mar 2018 18:39:52 -0000

--- v34
+++ v35
@@ -11,7 +11,9 @@

 1. __Atom selection__: atom selection that set the residues (see Resnames at [GUIMainwindow]) to be analyzed. Sterols must be not selected. __Default__: “not resname CHL1”.
-* __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. If more than one chain is selected, average of carbons with the same assigned index will be shown in the generated plot (but not in the .dat file ) __Important Note__:  lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
+* __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. 
+If more than one chain is selected, average of carbons with the same assigned index will be shown in the generated plot (but not in the .dat file ) 
+__Important Note__:  lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
 * __Leaflets__: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "-SCD vs Frame" plot.
 * __From__: initial frame number.
 * __To__: last frame number.

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Tue, 27 Mar 2018 18:38:08 -0000

--- v33
+++ v34
@@ -11,7 +11,7 @@

 1. __Atom selection__: atom selection that set the residues (see Resnames at [GUIMainwindow]) to be analyzed. Sterols must be not selected. __Default__: “not resname CHL1”.
-* __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. __Important Note__:  lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
+* __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. If more than one chain is selected, average of carbons with the same assigned index will be shown in the generated plot (but not in the .dat file ) __Important Note__:  lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
 * __Leaflets__: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "-SCD vs Frame" plot.
 * __From__: initial frame number.
 * __To__: last frame number.

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Wed, 26 Feb 2014 15:41:02 -0000

--- v32
+++ v33
@@ -19,11 +19,8 @@
 * __Output file path__: path to the output files, namely a "_filename_.orderparSCD" file suitable for external analysis, and a "_filename_.orderparSCD_plot~" temporary file containing -SCD values averaged per frame.

-##3. Tutorial

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

 _filename_.orderparSCD

ScdOrderParameter modified by Toni

Toni — Thu, 19 Dec 2013 15:48:06 -0000

--- v31
+++ v32
@@ -4,7 +4,7 @@

 ##1. Requirements
 __Lipid resnames__ definitions must be correctly set (see [Main Window](GUIMainwindow)).
-Also, see [General Requeriments](GeneralRequirements).
+Also, see [General Requirements](GeneralRequirements).

 ##2. Input
 [[img src=SCD_wiki.jpg]]

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Fri, 08 Nov 2013 10:05:37 -0000

--- v30
+++ v31
@@ -11,7 +11,7 @@

 1. __Atom selection__: atom selection that set the residues (see Resnames at [GUIMainwindow]) to be analyzed. Sterols must be not selected. __Default__: “not resname CHL1”.
-* __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. __Important Note__:  lipids different than phospholipids (e.g. sphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
+* __Acyl chains__:  selection of the specific lipid chain to be computed. See console output on a first dummy run for details on MEMBPLUGIN chain assignment. __Important Note__:  lipids different than phosphoglycerides (e.g. phosphosphingolipids) are likely to have different chain assignments. To avoid spurious average values always check the lipid chain assignment in your system.
 * __Leaflets__: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "-SCD vs Frame" plot.
 * __From__: initial frame number.
 * __To__: last frame number.

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Fri, 25 Oct 2013 10:53:27 -0000

--- v29
+++ v30
@@ -28,7 +28,7 @@
 _filename_.orderparSCD

 ~~~~~
-Leaflet Frame Lipid Chain ResID Residue Index Carbon -SCD
+Leaflet Frame Lipid Chain ResID    Residue Index Carbon -SCD
 0       0  DOPC        2    119        156  2  C22      0.043
 0       0  DOPC        2    119        156  3  C23      0.118
 0       0  DOPC        2    119        156  4  C24      0.171

ScdOrderParameter modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Fri, 25 Oct 2013 10:52:50 -0000

--- v28
+++ v29
@@ -28,7 +28,7 @@
 _filename_.orderparSCD

 ~~~~~
-Leaflet    Frame    Lipid    Chain    ResID    Residue    Index    Carbon    -SCD
+Leaflet Frame Lipid Chain ResID Residue Index Carbon -SCD
 0       0  DOPC        2    119        156  2  C22      0.043
 0       0  DOPC        2    119        156  3  C23      0.118
 0       0  DOPC        2    119        156  4  C24      0.171