Recycling Corner - Revision history

AngelHerraez: /* Visually transfer a hydrogen from a donor to an acceptor */

2025-08-10T18:26:17Z

‎Visually transfer a hydrogen from a donor to an acceptor

AngelHerraez: /* Rendering protein chain according to B-factor */ code update

2025-08-10T18:20:20Z

‎Rendering protein chain according to B-factor: code update

AngelHerraez: split contents into subpages

2025-08-10T18:14:51Z

split contents into subpages

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AngelHerraez: /* Rendering protein chain according to B-factor */

2025-08-08T09:54:33Z

‎Rendering protein chain according to B-factor

AngelHerraez: /* Rendering protein chain according to B-factor */

2025-08-07T18:51:59Z

‎Rendering protein chain according to B-factor

AngelHerraez: /* Rendering protein chain according to B-factor */

2025-08-07T18:44:35Z

‎Rendering protein chain according to B-factor

AngelHerraez: Rendering protein chain according to B-factor

2025-08-07T18:35:58Z

Rendering protein chain according to B-factor

AngelHerraez: /* Visually transfer a hydrogen from a donor to an acceptor */

2025-05-23T18:28:52Z

‎Visually transfer a hydrogen from a donor to an acceptor

AngelHerraez: /* Visually transfer a hydrogen from a donor to an acceptor */

2025-05-23T18:27:38Z

‎Visually transfer a hydrogen from a donor to an acceptor

AngelHerraez: /* Custom pop-up menus */

2025-01-24T17:04:33Z

‎Custom pop-up menus

@@ Line 524: / Line 524: @@
 == Visually transfer a hydrogen from a donor to an acceptor ==
-Script authored by [[User:Karsten Theis|Karsten W. Theis]].
+Script authored by [[User:Karsten Theis|Karsten Theis]].
 [[File:Grotthuss fast hires.gif|500px]] ''click to see animated''

@@ Line 565: / Line 565: @@
 First, apply the script that defines the function:
 <pre>
-function putty(s, grad) {
+function putty(s, grad) { // v.2
   define temp selected;
   select s and alpha;
-  bMin = {selected}.temperature.min;
+  var bMin = {selected}.temperature.min;
-  bMax = {selected}.temperature.max;
+  var bMax = {selected}.temperature.max;
-  wMin = 0.2; // trace thickness for lowest B-factor
+  var wMin = 0.2; // trace thickness for lowest B-factor (Angstroms)
-  wMax = 1.5; // trace thickness for highest B-factor
+  var wMax = 1.5; // trace thickness for highest B-factor
-  for (a in {selected}) {
+  for (var a in {selected}) {
-   a.trace = wMin + (a.temperature - bMin) * (wMax - wMin) / (bMax - bMin);
+   a.trace = wMin + (a.temperature - bMin) * (wMax - wMin) / (bMax - bMin)
+  }
-  if (grad=="wr") { // low B = white, high B = red
+ var c = "";
-  set userColorScheme [xFFFFFF] [xFFE0E0] [xFFD0D0] [xFFC0C0] [xFFB0B0] [xFFA0A0] [xFF9090] [xFF8080] [xFF7070] [xFF6060] [xFF5050] [xFF4040] [xFF3030] [xFF2020] [xFF1010] [xFF0000];
+  if (grad=="wr") { // gradient white > red (low to high B)
-   color trace property temperature "user" range @bMin @bMax;
+   c = color("white", "red", 32, false);
-  } else { // standard blue - white - red gradient (low to high B-factor)
+  } else { // standard gradient blue > white > red (low to high B)
-   color trace property temperature "bwr" range @bMin @bMax;
+  c = color("blue", "white", 16, false) + color("white", "red", 16, false);
+  }
   select temp;
+}
 </pre>
@@ Line 591: / Line 593: @@
   putty( {protein} );
   putty( {*:A}, "wr" );
-  putty( {*:B}, "" );
+  putty( {*:B} );

@@ Line 611: / Line 611: @@
 == Rendering protein chain according to B-factor ==
-This function will color protein trace according to the B-factor (temperature factor) of each alpha carbon and, at the same time, display ticker trace for the portions of highest B-factor. It was inspired by the "sausage" or "putty" rendering in Pymol.
+This function will color protein trace according to the B-factor (temperature factor) of each alpha carbon and, at the same time, display thicker trace for the portions of highest B-factor. It was inspired by the "sausage" or "putty" rendering in Pymol.
 First, apply the script that defines the function:

@@ Line 621: / Line 621: @@
   bMin = {selected}.temperature.min;
   bMax = {selected}.temperature.max;
-  wMin = 0.2;
+  wMin = 0.2; // trace thickness for lowest B-factor
-  wMax = 1.5;
+  wMax = 1.5; // trace thickness for highest B-factor
   for (a in {selected}) {
-   a.trace = wMin + (a.temperature - bMin) * (wMax - wMin) / (bMax - bMin)
+   a.trace = wMin + (a.temperature - bMin) * (wMax - wMin) / (bMax - bMin);
+  }
@@ Line 630: / Line 630: @@
    set userColorScheme [xFFFFFF] [xFFE0E0] [xFFD0D0] [xFFC0C0] [xFFB0B0] [xFFA0A0] [xFF9090] [xFF8080] [xFF7070] [xFF6060] [xFF5050] [xFF4040] [xFF3030] [xFF2020] [xFF1010] [xFF0000];
    color trace property temperature "user" range @bMin @bMax;
-  } else { // standard blue - white - red gradient (low to high B)
+  } else { // standard blue - white - red gradient (low to high B-factor)
     color trace property temperature "bwr" range @bMin @bMax;
+  }

@@ Line 615: / Line 615: @@
 First, apply the script that defines the function:
 <pre>
-function putty(s) {
+function putty(s, grad) {
   define temp selected;
   select s and alpha;
@@ Line 627: / Line 627: @@
+  }
-  set userColorScheme [xFFFFFF] [xFFE0E0] [xFFD0D0] [xFFC0C0] [xFFB0B0] [xFFA0A0] [xFF9090] [xFF8080] [xFF7070] [xFF6060] [xFF5050] [xFF4040] [xFF3030] [xFF2020] [xFF1010] [xFF0000];
+  if (grad=="wr") { // low B = white, high B = red
-  color trace property temperature "user" range @bMin @bMax;
+  set userColorScheme [xFFFFFF] [xFFE0E0] [xFFD0D0] [xFFC0C0] [xFFB0B0] [xFFA0A0] [xFF9090] [xFF8080] [xFF7070] [xFF6060] [xFF5050] [xFF4040] [xFF3030] [xFF2020] [xFF1010] [xFF0000];
   select temp;
@@ Line 636: / Line 640: @@
 Second, invoke the function for the part you wish to render in this style, such as:
   putty( {protein} );
-  putty( {*:A} );
+  putty( {*:A}, "wr" );
 == Custom pop-up menus ==

@@ Line 572: / Line 572: @@
 # Passing a variable from JSmol to a JavaScript variable:
 #: <code>myJSvar = Jmol.evaluateVar(myJSmol, myJSmolVar) </code>. Instead of the name of the variable, in the position of myJSmolVar you may use a Jmol math expression or some information from the molecule. <code>myJSmol</code> is the id/name of the JSmol object in the webpage (e.g. myJmol or jmolApplet0). [[Jmol_JavaScript_Object/Functions#evaluateVar|More details about evaluateVar()]].
 == Custom pop-up menus ==

← Older revision		Revision as of 17:04, 24 January 2025
Line 619:		Line 619:

	You can get this custom menu [[SimpleChem.mnu \| here]].		You can get this custom menu [[SimpleChem.mnu \| here]].
		+
		+	=== SimpleCryst ===
		+	[[image:SimpleCryst_menu.jpg\|right]]This is devised to ease the handling of the menu by inexperienced users with only basic tasks, in tutorial pages of crystallographic structures.
		+
		+	It includes just these entries:
		+	* Style - with simplified contents.
		+	* Color - simplified.
		+	* Spin - just with on/off, no axes or speed options.
		+	* Select - a bit simplified.
		+	* Show - space group, current state, symmetry, unit cell
		+	* Symmetry
		+	* Measurements
		+	* Console
		+	* Use full menu <sup>(*)</sup> - that allows to revert to the standard full menu.
		+	* Language
		+	* About
		+
		+	''(*) These are new entries, and so will not be localized; you may wish to edit them for your intended language.''
		+
		+	You can get this custom menu [[SimpleCryst.mnu \| here]].