H Add - Revision history

Pyadmin: 10 revisions

2014-03-28T01:47:06Z

10 revisions

Vinnyrose at 14:47, 20 June 2009

2009-06-20T14:47:54Z

Vinnyrose: moved H add to H Add

2009-06-20T14:35:09Z

moved H add to H Add

Vinnyrose at 14:05, 20 June 2009

2009-06-20T14:05:20Z

New page

[[h_add]] uses a primitive algorithm to add hydrogens onto a molecule.

= Usage and Algorithm Notes =
PyMOL fills missing valences but does no optimization of hydroxyl rotamers. Also, many crystal structures have bogus or arbitrary ASN/GLN/HIS orientations. Getting the proper amide rotamers and imidazole tautomers & protonation states assigned is a nontrivial computational chemistry project involving electrostatic potential calculations and a combinatorial search. There's also the issue of solvent & counter-ions present in systems like aspartyl proteases with adjacent carboxylates .

== Accessing Through GUI ==
[A]->hydrogens->add

== Syntax ==
<source lang="python">
# normal usage
h_add (selection)

# API usage
cmd.h_add( string selection="(all)" )
</source>

see also [[h_fill]]

[[Category:Commands|H Add]]
[[Category:Electrostatics|H Add]]

Bosmith: Cmd h add moved to H add

2007-10-05T13:03:54Z

Cmd h add moved to H add

Bosmith at 11:18, 5 October 2007

2007-10-05T11:18:30Z

Bosmith at 11:16, 5 October 2007

2007-10-05T11:16:43Z

Bosmith at 11:16, 5 October 2007

2007-10-05T11:16:34Z

Bosmith: New page: "h_add" uses a primitive algorithm to add hydrogens onto a molecule. menus [A]->hydrogens->add command line/console h_add (selection) via python A...

2007-10-05T11:01:04Z

New page: "h_add" uses a primitive algorithm to add hydrogens onto a molecule. menus [A]->hydrogens->add command line/console <source lang="python"> h_add (selection) </source> via python A...

New page
"h_add" uses a primitive algorithm to add hydrogens onto a molecule.

menus
[A]->hydrogens->add

command line/console
<source lang="python">
h_add (selection)
</source>

via python API
<source lang="python">cmd.h_add( string selection="(all)" )</source>

see also [[h_fill]]

← Older revision		Revision as of 11:18, 5 October 2007
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	see also [[h_fill]]		see also [[h_fill]]

−	[[Category:Commands]]	+	[[Category:Commands\|h]]

← Older revision		Revision as of 11:16, 5 October 2007
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	see also [[h_fill]]		see also [[h_fill]]

−	[[Category:Commands]	+	[[Category:Commands]]

← Older revision		Revision as of 11:16, 5 October 2007
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	see also [[h_fill]]		see also [[h_fill]]
		+
		+	[[Category:Commands]

← Older revision	Revision as of 01:47, 28 March 2014
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@@ Line 16: / Line 16: @@
 </source>
-see also [[h_fill]]
+see also [[H_Fill]]
 [[Category:Commands|H Add]]
 [[Category:Electrostatics|H Add]]

← Older revision	Revision as of 14:35, 20 June 2009
(No difference)

← Older revision	Revision as of 13:03, 5 October 2007
(No difference)