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Solve a small-molecule structure: Difference between revisions
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→assigning chemical types
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As a proxy to electron density we can use the refined ADPs. Atoms initially called "C", but with very low U values after refinement, are most likely O or N atoms. | As a proxy to electron density we can use the refined ADPs. Atoms initially called "C", but with very low U values after refinement, are most likely O or N atoms. | ||
For the H atoms, we just move the atoms from the bottom of the .res file to those lines where the refined atoms are, if the distances to existing (heavy) atoms are close to 1 A. For hydrogens bond to | |||
=== Hydrogens === | |||
For the H atoms, we just move the atoms from the bottom of the .res file to those lines where the refined atoms are, if the distances to existing (heavy) atoms are close to 1 A. For hydrogens bond to C N O (and in some cases B) we could alternatively use the HFIX instruction which sets up suitable AFIX instructions for the standard 'riding H-atom' refinement (shelXle - see below - can do this with one click). This requires lines of the form | |||
HFIX 13 XXX | HFIX 13 XXX | ||
In this example; the first digit 1 means tert-CH (2 would mean methylen-CH2, 3 would mean methyl-CH3, 4 would mean aromatic CH), and the second digit 3 means the normal riding model. XXX stands for the (heavy) atom name. For docs and more examples see [https://www.google.com/search?btnG=1&pws=0&q=hfix+shelxl]. | |||
=== Finishing the structure === | === Finishing the structure === | ||