Hydrogen bonds - Revision history

AngelHerraez: /* Calculation of hydrogen bonds */

2010-07-07T16:11:32Z

‎Calculation of hydrogen bonds

AngelHerraez: /* Display and rendering of hydrogen bonds */

2010-07-07T16:01:50Z

‎Display and rendering of hydrogen bonds

AngelHerraez: /* Display and rendering of hydrogen bonds */

2010-07-07T15:59:13Z

‎Display and rendering of hydrogen bonds

AngelHerraez: first draft of doc for calculatioj of H bonds -- needs work

2010-07-07T15:48:52Z

first draft of doc for calculatioj of H bonds -- needs work

New page

= Support for display and calculation of Hydrogen bonds in proteins and nucleic acids =

''Note'': this feature only applies to {{file|pdb}} format files of macromolecules (proteins and nucleic acids) -- or equivalent formats than supply all the needed atom and residue identification, like possibly {{file|mmcif}}.

== Display and rendering of hydrogen bonds ==
...

== Calculation of hydrogen bonds ==

In Jmol up to 11.8 there were just two ways to calculate hydrogen bonds: the RasMol way and a Jmol way. In both these cases these weren't really hydrogen bonds, they were what we can call ''pseudo-hydrogen bonds'' that do not involve actual H atoms.
* When the value for <code>hbondsAngleMinimum</code> was 0, Jmol used the RasMol calculation and ignored both the angle and distance checking.
* When <code>hbondsAngleMinimum</code> was set to something else, Jmol used its own calculation and did the angle and distance checking.

Jmol 12.0 introduces "true" hydrogen-bond calculation, and that changes the picture. The change is that if you have a pdb file with no H atoms and you do nothing special, Jmol will do just what it did before -- Rasmol hydrogen bonds. But if you want Jmol's calculation of pseudoHydrogen bonds, rather than obtusely setting the <code>hbondsAngleMinimum</code> value to something other than 0 degrees, you simply use
set hbondsRasmol false
Then <code>hbondsAngleMinimum</code> defaults to 90 and <code>hbondsDistanceMaximum</code> defaults to 3.25 for pseudo-hydrogen bonds and 2.5 for standard hydrogen bonds.

The choice of standard or pseudo simply revolves around whether hydrogen atoms are in the selected atom set or not.

← Older revision		Revision as of 16:01, 7 July 2010
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	Particularly, no bonds between amino acid side chains.		Particularly, no bonds between amino acid side chains.
		+
		+	(''check this!'') It doesn't matter whether the pdb file contains hydrogen atoms or not. The hydrogen bonds are found and drawn from O to N (in fact, you may find that the H atom lies slightly out of that line).

	Commands: ...		Commands: ...

← Older revision		Revision as of 15:59, 7 July 2010
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	== Display and rendering of hydrogen bonds ==		== Display and rendering of hydrogen bonds ==
		+	This is rather simple and dates back to Rasmol compatibility.
		+
		+	'''''Important note''''': not all hydrogen bonds are identified, only these:
		+	* Canonical hydrogen bonds holding the backbone in alpha helices, i.e. intrachain bonds between carbonyl oxygen and alpha nitrogen.
		+	* Canonical hydrogen bonds holding the backbone in beta sheets, i.e. interchain bonds between carbonyl oxygen and alpha nitrogen.
		+	* Canonical hydrogen bonds in Watson-Crick base pairs.
		+
		+	Particularly, no bonds between amino acid side chains.
		+
		+	Commands: ...
		+
	...		...

@@ Line 21: / Line 21: @@
 == Calculation of hydrogen bonds ==
 In Jmol up to 11.8 there were just two ways to calculate hydrogen bonds: the RasMol way and a Jmol way. In both these cases these weren't really hydrogen bonds, they were what we can call ''pseudo-hydrogen bonds'' that do not involve actual H atoms.
-* When the value for <code>hbondsAngleMinimum</code> was 0, Jmol used the RasMol calculation and ignored both the angle and distance checking.
+* When the value for <code>hbondsAngleMinimum</code> is 0, Jmol uses the RasMol calculation and ignores both the angle and distance checking.
-* When <code>hbondsAngleMinimum</code> was set to something else, Jmol used its own calculation and did the angle and distance checking.
+* When <code>hbondsAngleMinimum</code> is set to something else, Jmol uses its own calculation and does the angle and distance checking.
-Jmol 12.0 introduces "true" hydrogen-bond calculation, and that changes the picture. The change is that if you have a pdb file with no H atoms and you do nothing special, Jmol will do just what it did before -- Rasmol hydrogen bonds. But if you want Jmol's calculation of pseudoHydrogen bonds, rather than obtusely setting the <code>hbondsAngleMinimum</code> value to something other than 0 degrees, you simply use
+=== Jmol 12.0 ===
   set hbondsRasmol false
-Then <code>hbondsAngleMinimum</code> defaults to 90 and <code>hbondsDistanceMaximum</code> defaults to 3.25 for pseudo-hydrogen bonds and 2.5 for standard hydrogen bonds.
+Then <code>hbondsAngleMinimum</code> defaults to 90 and <code>hbondsDistanceMaximum</code> defaults to 3.25 for pseudo-hydrogen bonds (OÂ·Â·Â·N or NÂ·Â·Â·N) and 2.5 for standard hydrogen bonds (HÂ·Â·O or HÂ·Â·N).
 The choice of standard or pseudo simply revolves around whether hydrogen atoms are in the selected atom set or not.