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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 01:47, 28 March 2014
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