Backward compatibility - Revision history

AngelHerraez: Reverted edits by Reddyfox (talk) to last revision by AngelHerraez

2013-07-20T14:59:01Z

Reverted edits by Reddyfox (talk) to last revision by AngelHerraez

2013-07-19T08:15:56Z

‎Testing different applet versions

2012-02-21T10:21:03Z

changes in zShade

2011-09-21T08:44:05Z

"Testing different applet versions" moved to "JmolApplet" page

2010-12-13T17:42:37Z

‎Changed between v. 11.8 and 12.0

2010-12-13T17:16:16Z

‎Changed between v. 11.8 and 12.0

2010-12-13T16:43:08Z

new result of "hbonds calculate" in 12.0

2009-11-30T16:02:35Z

Testing different applet versions

2009-01-17T17:32:19Z

‎Hydrogen bonds: calculation and display

2008-10-09T11:47:19Z

backward compatibility - change in Hbonds on

← Older revision		Revision as of 14:59, 20 July 2013
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	See [[Jmol_Applet#Testing_different_applet_versions]]		See [[Jmol_Applet#Testing_different_applet_versions]]
−
−	~~Supported by [http://www.telsgroup.com/services/groupage_cargo_transportation_services/ TELS groupage].~~

← Older revision		Revision as of 08:15, 19 July 2013
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	See [[Jmol_Applet#Testing_different_applet_versions]]		See [[Jmol_Applet#Testing_different_applet_versions]]
		+
		+	Supported by [http://www.telsgroup.com/services/groupage_cargo_transportation_services/ TELS groupage].

@@ Line 11: / Line 11: @@
 * Changes in default behavior.
 Make sure to specify the old and new version numbers across which the behaviour was changed.
 == Hydrogen bonds: calculation and display ==

@@ Line 47: / Line 47: @@
 ''(This is an advanced feature)''
-You can force the use of a certain version of Jmol applet in any web page (even if that page is not yours). The way to do so is:
+You can force the use of a certain version of Jmol applet in any web page (even if that page is not yours).
-On the URL line of the browser, add
+See [[Jmol_Applet#Testing_different_applet_versions]]

@@ Line 16: / Line 16: @@
 '''Description:'''
-<code>hBonds calculate</code> fails to calculate hydrogen bonds on files that contain any H atoms.
+<code>hBonds calculate</code> fails to calculate hydrogen bonds on some pdb files that contain H atoms. The newer command <code>calculate hBonds</code> behaves identically.
 '''Effects:'''
-Old scripts using <code>hBonds calculate</code> will no longer display any hydrogen bonds in some cases.
+Old scripts using <code>hBonds calculate</code> will no longer display any hydrogen bonds in some cases (pdb-format files that contain hydrogens).
 '''Advice:'''
@@ Line 30: / Line 28: @@
 :The logic is this:
 :If you ask for <code>calculate hBonds</code>, now that Jmol has "real" hydrogen bond calculation capability (for all models, not just PDB files), Jmol will calculate H bonds for traditional PDB files (not containing hydrogen atoms) just as before, but if hydrogen atoms are included in the selected atom set, Jmol assumes you want actual hydrogen bonds, not "pseudo" hydrogen bonds between N and O atoms of a protein or nucleic acid.
 === Changed between v. 10.0 and 10.2 ===

← Older revision		Revision as of 17:16, 13 December 2010
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	Where you had the <code>hBonds calculate</code> command for a molecule, replace it with <code>select !_H; hBonds calculate; select all;</code>. Alternatively, use <code>calculate hBonds (!_H) (!_H);</code>		Where you had the <code>hBonds calculate</code> command for a molecule, replace it with <code>select !_H; hBonds calculate; select all;</code>. Alternatively, use <code>calculate hBonds (!_H) (!_H);</code>
		+
		+	:The logic is this:
		+	:If you ask for <code>calculate hBonds</code>, now that Jmol has "real" hydrogen bond calculation capability (for all models, not just PDB files), Jmol will calculate H bonds for traditional PDB files (not containing hydrogen atoms) just as before, but if hydrogen atoms are included in the selected atom set, Jmol assumes you want actual hydrogen bonds, not "pseudo" hydrogen bonds between N and O atoms of a protein or nucleic acid.

	=== Changed between v. 10.0 and 10.2 ===		=== Changed between v. 10.0 and 10.2 ===

@@ Line 13: / Line 13: @@
 == Hydrogen bonds: calculation and display ==
-'''Changed between:'''
+=== Changed between v. 11.8 and 12.0 ===
-v. 10.0 and 10.2.
+'''Description:'''
 '''Description:'''

@@ Line 1: / Line 1: @@
 Jmol intentionally keeps a strong backward-compatibility, that is, new versions try to maintain operative all things that could be done in older versions, with the same command syntax, and to also keep defaults.
@@ Line 5: / Line 6: @@
 This is a place to try and collect such discrepancies, for the benefit of the community of users and webpage/script programmers.
 Please, add here any issues you have found when updating Jmol versions:
 * Script commands that get broken when moved to a new version of Jmol.
@@ Line 25: / Line 27: @@
 Where you had the first <code>hBonds on</code> command for a molecule, replace it with <code>hBonds calculate</code>. Where <code>hBonds on</code> was only to restore display (e.g. after a <code>hBonds off</code>), you can leave it as it was.

← Older revision		Revision as of 11:47, 9 October 2008
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	Old scripts using <code>hBonds on</code> will no longer display any hydrogen bonds in most cases, or will display just a few of them (few pdb files include H-bonds specification).		Old scripts using <code>hBonds on</code> will no longer display any hydrogen bonds in most cases, or will display just a few of them (few pdb files include H-bonds specification).
		+
		+	'''Advice:'''
		+
		+	Where you had the first <code>hBonds on</code> command for a molecule, replace it with <code>hBonds calculate</code>. Where <code>hBonds on</code> was only to restore display (e.g. after a <code>hBonds off</code>), you can leave it as it was.