H Add: Difference between revisions
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(New page: "h_add" uses a primitive algorithm to add hydrogens onto a molecule. <b>menus</b> [A]->hydrogens->add <b>command line/console</b> <source lang="python"> h_add (selection) </source> <b>via python A...) |
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[[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 | [A]->hydrogens->add | ||
== Syntax == | |||
<source lang="python"> | <source lang="python"> | ||
# normal usage | |||
h_add (selection) | |||
# API usage | |||
cmd.h_add( string selection="(all)" ) | |||
</source> | </source> | ||
see also [[H_Fill]] | |||
[[Category:Commands|H Add]] | |||
[[Category:Electrostatics|H Add]] | |||
[[Category:Editing Module|H Add]] | |||
Latest revision as of 09:47, 20 June 2009
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