[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]
(This Webpage Page in No Frames Mode)

CCP14

Tutorials and Examples

Louis Farrugia's WinGX Single Crystal Suite

GUI based Hydrogen Addition using the SXGRAPH Program within WinGX and Shelxl97

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Tutorials page] | [WinGX Tutorial Index] | [SXGRAPH Tutorial Index]

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.

Adding Aromatic Hydrogens

Run 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).

Running SXGRAPH

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.

Selecting hydrogens by click and drag

Then via the top menu, select Model, Add Hydrogen, Aromatic C-H

Going into the Add Hydrogen Menu

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.

Going into the Add Hydrogen Menu

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

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.

Shelx refinement cycles completed with resulting summary screen

The following screen dump shows the hydrogen positions on the structure.

Structure with added aromatic hydrogens

Adding O-H Hydroxyl Hydrogens

In this case, we wish to add Hydroxyl hydrogens on the O9 and O3 oxygens. Use point and click to select the hydrogens within SXGRAPH.

Select the Oxygen atoms

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.

Structure with added hydroxly hydrogens

[Tutorials page] | [WinGX Tutorial Index] | [SXGRAPH Tutorial Index]
[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]
(This Webpage Page in No Frames Mode)
If you have any queries or comments, please feel free to contact the CCP14