SXGRAPH allows you to easily add HFIX insructions for adding hydrogens via the Graphical
User Interface. Following is an example based on Tetracycline for graphically adding
the HFIX commands, then doing a round of refinement whereby Shelx generates the hydrogens
and refines as per your requests.
The basic SXGRAPH procedure for adding Hydrogens, is i) select atoms, ii) use the "add-hydrogens" option and iii) do a round of refinement in Shelx and evaluate the resulting modifications to the structure. You can do multiple hydrogen addition commands before a round of refinement. For the purposes of this demonstration, we do one set at a time.
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Adding Aromatic HydrogensRun WinGX, load your structure, then run SXGRAPH by selecting the SXGRAPH ICON to (in the case of tetracycline) give you the resulting screen (thicker lines [using View Preferences] and atom labels have been selected as well).
At this point we want to add Hydrogen on the aromatic Carbons (C30, C33 and C26). We could just click on these 3 atoms to select them. However for this demonstration, enable the Box Selection option, them click and drag a box over the atoms to select them.
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Then via the top menu, select Model, Add Hydrogen, Aromatic C-H
You will then be presented with the Add Aromatic Hydrogens option. You can then select the type of constraints you wish to use depending on the quality of your data. Generating a Difference Fourier Map and trying to manually observe hydrogen electron densities could give you a good feel for the quality of the data with respect to Hydrogens. In this case, we will go with "Coords free - SOF and Uij fixed". Then either select the Save INS icon or File, Save INS File to save the changes.
Using the File, Preview INS menu option, you can see that the command generated by this graphical interaction was HFIX 42 -1.20 C26 C30 C33
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Select Refinement, Run SHELX-97 to process the HFIX command and refine the structure.
SXGRAPH will inform you of the status of the refinement on the bottom left hand corner of
the SXGRAPH screen. When the cycles of refinement are completed, a summary screen will be
issued which include any Warnings and Comments that Shelx may have generated.
The following screen dump shows the hydrogen positions on the structure.
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Adding O-H Hydroxyl HydrogensIn this case, we wish to add Hydroxyl hydrogens on the O9 and O3 oxygens. Use point and click to select the hydrogens within SXGRAPH.
From the main menu, select Model, Add Hydrogen, Hydroxyl O-H. Based of your knowledge of the quality of that data for locating hydrogens from the difference map, select the appropriate options (e.g., whether you want to locate the torsion angle from the electron density) and select OK. Select Refinement, Run SHELX-97 to process the HFIX command and refine the structure.
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