Hydrogen in macromolecular models: Difference between revisions
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[[PDB files]] that you save from either of these methods, can, for example, be uploaded for visualization in [[FirstGlance in Jmol]]. | [[PDB files]] that you save from either of these methods, can, for example, be uploaded for visualization in [[FirstGlance in Jmol]]. | ||
===Test Results=== | |||
[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms. The results from the above two servers: | [[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms. The results from the above two servers: | ||
{| class="wikitable" style="text-align:right" | {| class="wikitable" style="text-align:right" | ||
|+ | |+ Results for 1d66 | ||
! Server !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens | ! Server !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens | ||
|- | |- | ||
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|- | |- | ||
| WHATIF || 1,000 || 423 || 102 || 1,525 | | WHATIF || 1,000 || 423 || 102 || 1,525 | ||
|- | |||
| Jmol || 990 || 427 || 0 || 1,417 | |||
|} | |} | ||
'''1d66:''' WHATIF protonates the sulfurs in 12 cysteines that are coordinating 4 cadmium ions, and the 2 N terminal nitrogens (6 H atoms), while MolProbity does not. MolProbity protonates the terminal hydroxyls on the 2 DNA chains, while WHATIF does not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not. | '''1d66:''' WHATIF protonates the sulfurs in 12 cysteines that are coordinating 4 cadmium ions, and the 2 N terminal nitrogens (6 H atoms), while MolProbity does not. MolProbity protonates the terminal hydroxyls on the 2 DNA chains, while WHATIF does not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not. | ||
MolProbity and WHATIF were tested in 2008. Jmol was tested in 2026. | |||
