Difference between revisions of "H Add"

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"h_add" uses a primitive algorithm to add hydrogens onto a molecule.
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[[h_add]] uses a primitive algorithm to add hydrogens onto a molecule.
  
<b>menus</b>
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= Usage and Algorithm Notes =
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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 .
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== Accessing Through GUI ==
 
[A]->hydrogens->add
 
[A]->hydrogens->add
  
<b>command line/console</b>
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== Syntax ==
 
<source lang="python">
 
<source lang="python">
  h_add (selection)
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# normal usage
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h_add (selection)
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# API usage
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cmd.h_add( string selection="(all)" )
 
</source>
 
</source>
 
<b>via python API</b>
 
<source lang="python">cmd.h_add( string selection="(all)" )</source>
 
  
 
see also [[h_fill]]
 
see also [[h_fill]]
  
 
[[Category:Commands|h]]
 
[[Category:Commands|h]]

Revision as of 17:35, 9 September 2008

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

# normal usage
h_add (selection)

# API usage
cmd.h_add( string selection="(all)" )

see also h_fill